Torch bug paste (complete scoundrel) is good if you can hit him. It's a splash, so there's a decent chance of that.
Unless he is flying, so you can't hit his square (since he is floating in mid-air there is nothing for the splash weapon to smash against).
The real trouble here is dealing with invisible flying opponents w/ fast healing, and since a regular Imp can do just that. I would like to note that level 2 parties should be able to deal with such threats. The 3 levels of cleric, while nice, doesn't add enough to this imp that it goes overboard, since it can only cast 2 second level spells, gets very little from healing itself, and generally don't want to be in a situation to cast inflict wounds, so all it really can do with those spells is summon things.
Alternatively it could attempt to augment the aberration it summons, but even that isn't that powerful IMO.
So I don't think this is a flaw in the CR system, and agree that this is a CR 4 encounter, which is what the CR system sets it at.
The DM, in this encounter, does however seem to have buffed it's AC arbitrarily, unless it was under the effects of both a shield of faith and a Cats Grace spell, in which case it would only have a single 2nd level spell left, and most parties should be able to not be engaged by it.
A simply creature, such as a Tiger (that is also CR4) Could charge in from hiding (which it has a +11 bonus to in it's natural environment), and pretty much kill one PC in that round, then it would have to be shut down, with a spell or a lockdowner or it would be able to pretty much kill one character per round. CR 4 encounters are this dangerous when you are level 2, this is how it should be IMO.