I think the situation you're describing isn't really about assessing the difficulty of a skill check.
It's more about warning the PLAYER that an intended action might be more risky for his character than he thinks. In similar situations I often tell the player something like "Your character has a feeling this might not be a good idea. Do you still want to try it?"
It's often a case of a player forgetting about a certain rule or overlooking something about a situation which his character wouldn't have been able to miss.
I
think there are rules for utilizing Sense Motive to judge the power level of another entity relative to yourself in one of the skill-heavy splatbooks. Of course, you can only judge them by what you can detect, so, barring magic items or active spells to learn more about an entity, you're limited to what you can see and/or hear.
Offhand, I don't remember which book, but the most likely contenders are probably Complete Adventurer, Complete Scoundrel, Song and Silence, or the Epic Level Handbook (why they kept the non-epic usages they added there out of the skill section of the SRD is beyond me).
From what I remember there were something like 5 possible accurate judgements: Similar(within 1 or 2 levels/CR/EL), Stronger(2-5? levels/CR/ELhigher), Weaker (2-5 levels/CR/EL lower), Near Impossible(5+ levels/CR/EL higher), Pathetically Easy(5+ levels/CR/EL lower); failing the check gave an incorrect result; you could apply a similar scale to other related judgements.
If you can't find it, one method I've seen used before is the GM rolls a d100, and asks the player High or Low, if it matches, they get an accurate statement from the GM, if it doesn't .. they usually get nothing (but if it's different and the roll was 1-5% or 96-00%, they misjudge the situation). Sometimes, Wisdom is applied to the roll most beneficially to the player.