Nice work from PCat. I'd say that is right down the right lines.
I've run something fairly similar to what you are talking about. The group had failed their 3rd skill check on a very complex challenge 12/3 in an attempt to destroy the altars in thetemple of an evil god. They had 8 successes when they rolled up the third failure. The attempt to correct this failure (Involving damaging the temples complex light filter system) resulted in a critical 1... so there was no turning back. The god's ire awoke and he began to bring the temple down on the pcs heads as heads.
We broke off the game at that very tense point, a lot of things were going on. The god who had manifested through a dark ritual his followers (killed by the pcs) had invoked had surrounde his altars with shadow minions to protect them. So there was round by round fighting going on apart from the challenge.
Also the temple was split into 3 levels, the altars divided between levels, so movement became very important.
Between sessions, the player of dwarven cleric who was responsable for the failed roll that damaged the vital light filter system, told me she had intentions to stay and try and repair the filter system with the Repair ritual. I thought that sounded like fun. So...When we came back I asked each pc what their intentions were and based on their response, gave them explicit information on one of three challenges they would have to face. Many chose simply to flee, so they got the 'Flee for your life Challenge'. 4 decided to stay so they got the 'Glorious Death Challenge'. One player wisely said she wanted to uninvoke the presence of the evil god, which was the key to either of the other challenges, and she got the 'Send Auxlatl home challenge'.
Several factors going on increased the tension. Every round it became increasingly difficult to move as the tremors intensity increased. Also the falling debris damage that resulted from a failed SThrow at the beginning of each round increased round by round.
Fleeing was an individual challenge, but players could cooperate and work together to make escaping easier.
I made the goal of the repair challenge to reduce the time of the ritual from 10 minutes to 10 rounds. Certain successes could reduce the time even further.
The easiest challenge was to reverse the dark ritual which would buy them 4 rounds of total calm to either flee or complete the ritual safe from danger.
Also there were many secondary skills a player could use that didn't result in successes but protected from the hazards of the temple and the ire of the furious god.
Succeeding with the Repair ritual removed a fail from the original complex challenge, which they then had to continue from where they left off.
Maybe you could include some of these elements in your skill challenge.
As PCat suggests, once a certain point in the main challenge is reached combat is triggered and the PCs are set upon by wave after wave of minion hordes. The PCs have to hold them off until a certain task is achieved (which would depend on the enviroment and how the pcs are trying to manipulate it to their advantage). Skills and battle being used simultaneously. Maybe they are trying to reset an ancient trap they have found which would block off one of the main corridors leading to the groups ritualist. You could run a minor separate skill challenge til this is achieved.
My group had a key object that allowed a one time use to speed up the ritual; the object was the holy symbol found on the body of the evil god's dead sister. Perhaps some key history checks could reveal an arcane santuary in the area where a minor 'mental skill challenge' (dungeoneering, history, arcana, thievery, religion) can be run to unravel the arcane locks and enter. Inside the energy aids the ritualists concentration, heightening his memory and reducing the time necessary to cast the ritual.
The time needed is cut down to a certain amount of rounds. Maybe when this begins the intrusion awakens the sanctuary's arcane guardians, the environment turns against the intruders and the and the challenge becomes surving in the hostile yet useful environment for that length of time. The challenge could turn towards appeasing the arcane guardians. While this goes on numerous secondary skills could be useful to protect the ritualist from attacks, avoid the hazards of the environment or reach the key points with difficult movement (climbing, jumping, swimming, balancing, swinging) in order to do whatever is necessary to shut down the guardians.
A challenge like this is complex. But it can be very fun, dangerous and tense, and everyone should have a chance to shine in it.
