The thing is, though, the Rogue really wasn't doing much work there aside from the starting damage bonus; you didn't even use his inherent first strike to finish off the boss. You could have pulled the same exact strategy off with a Berserker, and the only loss would be the 20% dodge - but since you wouldn't have first strike you could actually exploit your dodge prediction more easily (attacking any of the level 1s would have given you a hit and another chance to dodge). You could have done the same thing with a Warlord, too, and would have had the added benefit of guaranteed, repeatable CYDSTEPP and used your mana potions for extra damage bonus (and some phys resist reduction if you got Tower of Goo). And any other class could pull the same thing off with slightly more resources, since again the only thing they're missing is the damage bonus.
It seems to me that this is more the result of a (relatively) careful manipulation of several different elements of the game in order to achieve a powerful result, and not a sign that any one of those things is overpowered. (Although I do think Tikki Tooki's potion boon could stand to be adjusted, and I stand by my repeated comments that Rogues would be much better at 7-8 HP/lv and something like 20-30% damage bonus or 15-20% and +15-20% at full HP. As for the potion preps, well, IMO preps are this game's equivalent of cheat codes anyway so I have no comment. The Trisword, of course, is just silly, but it's always been silly.)