Stop, step back, take a deep breath, and think.
What are you trying to achieve with this game? Are you:-
(a) Telling the players a story which you have already figured out in your head, or
(b) Running an interactive game in which the players' actions can alter the outcome.
Now, some DM's run games which are almost pure (a); they will act to preserve their carefully-planned plotlines no matter what spanners the PC's throw in the works. A bad DM of type "a" would have this NPC improbably rescued from death via some power or magic item, or suddenly introduce an evil NPC High Priest who raises his body (NB: this works once. If you do it often, the players will learn that when they kill an important NPC they should burn the corpse and scatter the ashes over the ocean, and this is what they will start to do).
However, this is a heavy-handed approach. The message that it sends to the players is "You cannot mess up my plotlines; if you try, I will make something happen to preserve the plot." It tells them that they cannot have any impact on important outcomes. If you're going to act in this way, there's no point playing it out as a game. The players might as well just sit around drinking beer while you tell them what happens.
A good DM of type "a" would permit the NPC to die, but would act to preserve his plotline in such a way that his actions were invisible to the players. The next person in line to run the Thieves' Guild would be a noticeably different NPC, but who nevertheless shared the old GL's aims and objectives (personally I'd make it the existing GL's girlfriend who's read his diary and knows what he had planned).
A DM of type "b" would react to the situation by immediately abandoning the plot. There's many sessions worth of mileage simply in administering the consequences of the PCs' actions.
For example, the result might be upheaval and turmoil in the Thieves' Guild as the different possible successors all scramble for leadership. Divide the Guild into two or three factions and set them warring among themselves; but one of the few things upon which the Guild can agree would be that the murderers of the old GL need to be caught and punished, so have them set a huge price on the PCs' heads. Of course, being aware that the former GL was butchered, these people will do their utmost to eliminate the PC's without the PC's ever becoming aware of who they are, let alone where to find them.
In the meantime, the Thieves' Guild informs the law of the murder and demand that the characters be brought to justice. Since they have the ear of a corrupt judge, a warrant is issued locally for the characters' arrest - in other words, they're on the run from the Guild and the law at the same time.
I advise combining these two approaches.
In the short term, abandon all hope of progressing the plot. The characters have done something big - so you should make them feel that they've affected things. They need to see big changes in the world that arise directly from what they did. There's open warfare between Thieves' Guild factions on the streets, which the players can get involved in if they like (but they shouldn't yet see that it's a stacked-deck contest; the old GL's girlfriend is the one who's likely to win, largely because she is the one who - instead of calling for the PC's to be executed - offers them a fat bribe to join her side!) There are revenge attempts, officers of the law knocking on their doors late at night, grateful merchants giving them discounts in the stores, the whole nine yards.
In the long term, of course, you're preparing to take the plot in the same direction it was always headed.