I think you've heavily overstating how common they are. A couple of lost strength and toughness from advanced undead don't ruin a character. I was a new player too (can't get away with calling myself that these days, admittedly), and I never felt that these creatures were too common or would inevitably ruin my day when I met them. I just learnt to deal with them. It might have turned out different if you regularly met wights etc. in the small cave or village dungeon, but no - you find those guys in the midgame at the earliest. You'd have to be colossally unlucky to meet a vampire until the CoC graveyard, and even then I wonder how you'd get anywhere near that far with a "low DV warrior". On the list of top 100 things that are going to screw you in ADOM, stat drains don't even make, like, the lower sixties.
Strength drains are already temporary in the sense that training strength back to at least 18 is easy, especially if you've been there before (i.e. your potential is higher). Toughness drains, morgia roots, plus the corpses of the undead that drain stats. Greater daemon stat drains can affect hard-to-fix stats, but then the greater daemon is a boss fight. With a daemon. That's supposed to be a somewhat nasty affair, isn't it?
Consequences are not a bad thing. I played XCOM: Enemy Unknown, the reimagining of the old classic X-COM: Ufo Defense, recently (a great game, by the way). Your soldiers, who grow in power as they rise in rank and in some way represent your own "stats", will frequently die to aliens, more often than not because you made a strategical mistake; sometimes just because aliens are nasty like that (really, though, it was probably a mistake of yours even then). And yet, the game includes an Ironman mode in which there's only one savegame and dead soldiers are permanently dead, and it's played by more players - exclusively - than even the designers anticipated, who added the mode as an afterthought and hadn't expected players to actually want to subject themselves to permadeath. Then there's the success of FTL, which borders on mainstream - and places an equally high emphasis on deadliness and consequence. It's making a comeback, and ADOM is just in time.
What this tells us is that consequences are not a bad thing; they add to the experience since they lend weight to the decisions you make in the game. Permanent stat drains would be bad if they were unavoidable and make no sense within the game's world; but they're usually neither. There are a select few monsters that can even drain stats, and they all make sense. Vampires and wights and spectres and wraiths should be terrifying and imbued with undead malicious magic that feasts on your life force. And more importantly, stat drains need to be felt by the player, who's expecting the world of ADOM to be hostile and dangerous, or they'd lose all meaning. If you make them temporary, you'd have to make them bigger so they actually become dangerous short term, or you might as well not bother.