To be honest, even though you won't see autopsy tables throughout the rest of the game, the "creepiness" factor never really lets up. You might get used to it, or you might not.
The best explanation I can think of is that the game is about MORTALITY. That means it's about flesh and blood, among other things, and those things decay. In Sigil, things happen just because people BELIEVE in them, so you end up with things like walking corpses and people who can swap out teeth and eyeballs and so forth. However, in Planescape Torment's defense, even if things are macabre, there is always a sensitive, humane underlying element. For example, you might meet a zombie later in the game who is weeping. She has feelings, and she is obviously very upset something. If you can look past the fact that she doesn't have tear ducts anymore and there's something else oozing out of her eyes, you might feel sympathetic. Even though she was a zombie, I was rather touched by her predicament. None of the companions who can join your group are human, and it's questionable whether the main character is human anymore after what he has done to himself (or what has been done to him, which is what you're supposed to find out). But you'll never question their "humanity", so to speak. After playing Planescape Torment, you might see things in a new way.
It's not like other roleplaying games. Instead of killing everything you meet and running up a body count as high as possible, you can spend your time reading about philosophy (there are fifteen different "factions" in Sigil, all of which have unique beliefs) and solving mysteries and helping people. To me, the lesson is that you should have respect for both the living and the dead. I only attacked other creatures when I was being attacked (although, if you want to put yourself in a position where you can kill a bunch of monsters for lots of experience points, you can do that).
I just want to emphasize again that the game really gets down to the nitty-gritty, so to speak, and it can seem rather bizarre. It might indeed be challenging to look past that. Personally, I didn't exactly enjoy the more gruesome elements, but sometimes I found them fascinating. Sometimes they're a bit funny. For example, your main character can't die permanently, so he asks other characters to do things to him that are a bit violent. For example, he thinks that something might be hidden somewhere in his body, so you have the option to ask another character to split his skull open and look inside. Things like that are so unexpected to normal people like us, you'll either find it disgusting or think it's kind of interesting. Or maybe after playing Planescape Torment, you'll just take things like that for granted.
By the way, here are my recommendations for stats. Start with:
STR 9
DEX 13
CON 9
INT 14
WIS 18
CHA 13
...or as close to that as you can. Every time you level up, you can add a point to one of the stats, all the way up to 25. Wisdom is the most important stat because it gives you the best dialogue options (if your Wisdom isn't high enough, you won't see all of the options), and if you have high Wisdom, you get experience point bonuses (up to 35% extra every time you gain experience, I think). There are also items in the game that raise your stats, and you get extra stat points just for
talking to certain people. That's because your character, who is thousands of years old, can recover his old abilities when he starts to regain his memories. If he can recover enough memories, he has the potential to be almost god-like. I wouldn't worry too much about stat points, because you'll have plenty in the end.
When you level up, here's what I would add to each stat:
STR none (use items if you need them)
DEX max out at 16, then use items if you need better Armor Class
CON none (make sure you get maximum hit points every time you level up)
INT start with 13 or 14, use tattoos to raise it to at least 16, and add points until you're up to at least 19 (23 is optimal)
WIS add one more point if you start with 18, then follow the quests for other stat increases (24 is optimal)
CHA start with 13, raise it to 14, buy a tattoo to raise it to 16, then follow quests to raise it a couple more points -OR- max out if you prefer (23 or 24 is optimal)
As you can see, I think Wisdom, Intelligence, and Charisma are the only stats worth worrying about. Your character doesn't need to get into a lot of fights, you can let your NPCs serve as bodyguards if you like, your character always gets right back up if he dies, and he regenerates hit points pretty fast; so I don't think Strength, Dexterity, and Constitution make any difference. (There are a few dialogue options where it's nice to have Dexterity over 13, and it's nice to have better AC so you don't get hit, but other than that, a Mage doesn't need high Dexterity.)
Talk to everyone you can (just examine the Mortuary zombies, don't try to make conversation with them unless you want to be chaotic), read every book you can, look at every item description carefully, and think about your dialogue options carefully. You'll get more experience and stat points than you thought possible. There's a LOT of information to keep up with, but I found it very rewarding.