I cannot explain how the studio responsible for two great sequels made a prequel that I can't stand to play.

Part of it was that they were learning how to make a D&D game; I believe Baldur's Gate was their first real attempt, and the first serious attempt at a reimplementation of the pen and paper rules since the Gold Box games.

My problems: the starting difficulty was very high for a spellcaster class. One unavoidable encounter puts you against a mage who can start battle with a volley of five magic missiles (if I recall correctly). This will guaranteed kill the PC, ending the game.

That's just the underlying rule set being a bitch. First level characters are fragile and die a lot in the paper game. We used to roll up big batches of them, see which ones survived, and then start to make up backstories for them around third level. BG1 has that same fundamental issue to deal with, the fact that first level AD&D characters are supposed to die all the time. In the paper game, you could just make lots of characters, but in the computer game, you have to use save and reload.

For that specific thing: as /u/Waswat says, you could use the Shield spell, which is first level. That makes you immune to magic missiles. If you're a cleric, well, I'm not sure what to do. Although I think you might be misremembering how many there were; five magic missiles would take a 9th level mage to cast, and I doubt they'd throw someone that powerful at a first-level party.

The mines stage is a very steep difficulty step up, all the more because you can't rest or you'll be attacked.

I used quicksave/quickload savescumming to work around that problem. You don't have a very high chance of successfully resting in the mines, but quickload makes all things possible.

which had properly scaled encounter difficulty levels,

Again, that's an artifact of the rule system they were using. That's what a first level AD&D adventure really looks like. It starts to get better around third level, but levels 1 and 2 are brutal.