Watched Rory's fight with Condit again a few minutes ago and for a guy who was winning the fight, Rory did very little damage to Condit either standing or on the ground.
Now look at fights that Penn lost by stoppage (hughes and GSP) both in round 4 or came close ( Diaz and Fitch) only in round 3. At no stage in these four fights did a single strike on it's own have Penn in trouble, the accumulated effect of the fight wore down Penn for someone else to step in to stop them or the fight finished before it could be stopped ( ie his corner would have not have let him out for round 4 against Diaz had it been a 5 round fight and think the ref would have stopped it in the fourth against Fitch had it been a 5 rounder)
Also Penn usually wins the first round of fights, 3 of the 4 mentioned above for example, and starts the second well before starting to fade. This leads me to think that your prediction of a 2 round stoppage is a little early in the fight.
If I was to bet on Rory winning by TKO it would be in the 3rd
Personally I think that if this fight is stopped it will go against Rory, in his fight against Condit when it went to the ground in the first 2 rounds Rory was on top looking to ground and pound. Condit was able to tie Rory up with his guard to limit the damage taken, Penn is very similar in his ability to do this from his guard. Rory also doesn't look to have a one punch knockout power and with Penn having been a former world BJJ champ I can't see Rory submitting him and with the fight only been 3 rounds I think Penn will be the winner if the fight finishes early and Rory the winner if it goes the distance in a close decision.