This isn't Dungeons and Dragons. Undead are not always evil or powered by evil spirits/negative energy. There have been plenty of examples of neutral and friendly undead. It doesn't HAVE to use this convention. This series didn't use that convention until D:OS 1.
In fact this game doesn't even follow its own conventions. You are a skeleton-type undead, not a zombie-type undead. Skeletons shouldn't have the Zombie talent at all (they didn't in D:OS 1 at least).
You're correct. The Divinity series *isn't* D&D, but it sure borrows a lot from it in use in the game's design. Games like Final Fantasy did as well, a JRPG that also has a system where holy magic such as curative spells have negative effects on undead; you see this used time and time again not only traditional CRPG's, but also JRPG's. They even emulate these tabletop mechanics it in their very own "GM mode" by allowing for dice, vignettes and traditional P&P storytelling and game-play, so you shouldn't deny the fact that they've taken more than a few ideas and built parts of their game in homage to these systems; it's no sin to borrow from other source material as long as you make it your own, which I feel they have.
What is boils down to is the lore of the game. If the team, and loremasters at Larian Studios believe that undead should be harmed by 'positive energy' or whatever these spells are considered, then that's how it's going to be, since it fits into their lore. Yes, this may make the game a bit more difficult, but in a number of situations, it makes it easier if you look at the perks that undead *do* have. They even give a warning that it'll make the game more challenging before you play an undead character.
Does it suck for people who wanted a more traditional character race that they could play alongside their friends, and benefit from the same boons that the rest of the party has? For sure. Does it make them any less fun? That's subjective. With that said, it by no way limits you from playing with other races in the same party. Yes, it may be difficult in some places, but we play games to be challenged in most cases, don't we? Isn't that what makes them fun?