Little has been said so far about the portal by the original poster ...
Is it a well known and official trade route between the cities? If so I expect it to be heavily guarded - like a more typical gate, such as the one leading to the local lord's palace or the noble district of the city. Getting to the portal - and managing to determine how it is activated - should almost be an adventure all by itself. Then there are the guards on the other side of the portal to worry about. And surely information on recent major crimes go back and forth through the portal. If caravans make use of it, I presume that they are very thoroughly checked by the guards, and that thieves are ever attempting new ways to send things (and people) through without the guards being aware. The PCs are likely to need significant help or incredible battle prowess to get through the portal - only to face more guards (with plenty of reason to be suspicious) on the other end.
Or perhaps the local thieves guild has an in with the special order of guards that protect the portal, who have over the years secretly become a bit corrupt and are willing to let people secretly make use of it for a specific bribe or a signed waiver from the thieves guild who regularly tithe them.
Or perhaps it is relatively unknown, used only by the local mage's college as a means of travel between it and a magical university in the other city. High ranking lords can use it - for a price, and illusions and such are used to confuse them into thinking a temporary means of translocation is in use (some incredible ritual) rather than a continuously open portal. Or perhaps only a single word in the long ritual is actually needed to open the portal, and some minor wizard functionary at the college has recently realized which word is actually needed. He may be willing to help the PCs escape, for a price. Or perhaps he wishes to leave with them, hoping to find a better life (or a better chance for advancement) at the other magical college, which may have a rivalry with this one. Wizards on the other side may take advantage of this youth to gain secret knowledge of this side's wizards and the college. The PCs may be allowed to live and leave for a price (perhaps sent on a potentially dangerous quest to find some unusually material components, with a geas used to make certain they fulfill their side of the agreement).
Or perhaps only the largest thieves guild has such a portal. The cities involved are almost ancient, and the guild stumbled over the portal during its explorations of the underside of the city, finding an old store room under a cellar of what once was a palatial residence belonging to a powerful wizard hundreds of years prior. They use it to work / exist in both cities at once, stealing in one city and fencing in the other city, and vice versa. The head of the thieves guild and his equivalent (or his viceroy) in the other city are the only one who knows the secret of how to operate it (and uses this knowledge to keep from getting killed by his minions, who do not wish to lose use of the portal). He is willing to aid some who aid his guild - for a price (here or in the other city). Or maybe the portal (and its means of activation) have only recently been discovered, and he is willing to use the PCs as guinea pigs to see if it works normally or has some potentially dangerous features as yet unknown.
Another idea that comes to mind: the portal is larger than the city guard realizes, extending under the ground as well. The local thieves have realized this and use it to move between some forgotten section of sewer or cellar beneath the portal area to a similar area in the other city whenever the city guard officially make use of the portal. They may be willing to help the escaping PCs hide away for a time until the portal is next openned - and then let them through for a price to be paid in the other city. Or perhaps no one has yet realized this truth of the portal, and the PCs - escaping through the sewers towards the portal area, happen upon the under-portal while the over-portal is open, escaping unknown to the other city. How will they make use of this incredible and currently unknown to all else knowledge?
Any of this work for you?
---------------------------------------------
Another idea occurs to me.
What if the portal is powered not by magic but by life? Everyone who uses it takes 1+1d3 Con damage. Or perhaps they lose 2 points from a random ability - each player rolling 1d6 to determine which ability. Perhaps the portal is rarely used for this reason, as it takes a few days before those who used it might safely return to the other side (presuming the portal is well known and used by both cities).
Or maybe the portal's creator is still alive, and its use triggers a mental alarm leading to the creator scrying the party. If the portal is rarely used (or has not been used prior in years / decades / centuries), this may interest its creator. The PCs might be told that they feel as if they are being watched, after they leave the portal area.
Or perhaps the portal was created for a specific purpose, and all who use it automatically have certain spells cast upon them as they exit the portal, perhaps even a minor geas. The PCs might be inconvenienced by these spells or even slowly debilitated (if a lesser geas is in use) until they use a divination to learn what is wrong with them and what to do about it.
Or maybe the portal is destabilized by something the PCs are carrying - and they end up *near* the other city (as if by teleport rather than greater teleport). They now must determine where they are, which direction and what distance to the nearest civilization (the other city) and work their way through the wilderness for a few days or weeks to reach the other city. On the plus side, there will be less reason for them to initially be suspected as the criminals who fled through the portal. On the negative side, there has been plenty of time for news of the crime to be circulated throughout the city, the tale growing larger with every re-telling - and their pictures placed in several inconveniently prominent locations. Might be time to dust off any disguises they've used in the past.
