Well, without knowing the numbers (the search DC the Disable device DC and the bonuses the rogue had to those skills, as well as his HP and his reflex save) I can't really judge if it was a 'fair' encounter. But, that's not really the question.
In the original question, you asked if the Rogue's trapsense would come into play. The short answer is no (because you have eliminated the two things to which it applies, namely a save or an attack roll).
But, if you want to get a feel if this is fair, think of it like a monster and use the party's frontline PC as an example. Let's (wildly) assume the rogue has 20 HP so 3D6 damage will on average put him at about half. Let's also assume the front-liner has maybe 40.
Ok, would you allow this situation?
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The party is advancing down a long tunnel cut into the stone below an old wizard's keep. They think there is a secret escape tunnel into the keep and are trying to find it. As they turn a corner a gate falls from the ceiling, isolating the Paladin (who happened to be in front). At the same a sidewall opens and reveals a large mechanical man carrying a huge axe. The thing is mumbling to itself confusedly.
Now, in game terms the mechanical thing is a golem of some variety, and it is holding an axe that does on average 20 points. If the paladin must make a sense motive check to know that it's master has died and that it is waiting for orders. If the Paladin doesn't make this check he will not be able to make a diplomacy check to convince the beast that he is the new master.
Of the Paladin fails the sense motive check, or fails the diplomacy check he will be attacked. There is no attack roll and no save, the monster just automatically hits the paladin for on average 20 points and then goes back to standing there.
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So, in this example, the automatic hitting is revealed as excessive. Not imagine that there are three of these things (though only two will attack). It's getting harder isn't it?
It may be that you think this is fine, and that's a judgment call. I, for one, would allow some kind of save / attack roll or would up the DC by a lot.
Notice that; the paladin can take 20 on the sense motive check (as the rogue can take 20 on the search). I mean BY THE GODS folks, Knifespeaks actually posted recommending taking 20! The seas, they are boiling!
Also notice that the Paladin can't take 20 on the diplomacy check, just as the rogue can't take 20 on the disable device check.
Ok, there's one flaw, the rogue doesn't have to deal with the traps, he can just leave them. So let's add that the Paladin is fairly sure he can beat down the gate separating him from the group.
Anyway, what do you think? Would you allow this situation?
-Tatsu