I would allow arcanists to use magic-missile at will. I won't, but I wouldn't have a problem with it. If you want to balance the class, take away the familiar in exchange.
Hear me out:
I've played arcanists a-plenty, and although it was always on my spell list, rarely used magic-missile. I only use it as a last resort, when all other options fail, and generally fighters do from 2 to 5 times more damage per round than I can with magic missile.
Here are a few balancing points:
If you do that, magic missile becomes a spell-like ability, and thus cannot be boosted by metamagic feats.
Since it doesn't require a to-hit roll, rogues can't use it for sneak attacks.
It is still subject to spell resistance.
Although it always hits, at first and 2nd level it does the same average damage as a crossbow bolt. By third level, you're better off with scorching ray. At mid to high levels, you'll almost never use it (especially sorcerors).
It is completely useless against creatures with total concealment. Not so with a missile weapon.
If you want to limit it somewhat, make casters make a spellcraft DC 10+caster level check to successfully launch the magic missile. One missile: DC11; two missiles: DC13; three missiles: DC15; four missiles: DC17; five missiles: DC19; of course, the targeted caster level cannot be higher than your own.
There's also the problem of captured PC's. A wizard would always be armed. I don't see this as a real problem, because a sorceror is always armed anyways. If you capture a party, the next morning the sorceror regains all his spells, and although all the party's equipment is taken away, the sorceror can still cast all his spells that don't require material components.
Which is why captured arcanists are usually bound and gagged. And if my proposed arcanist is, he can't cast his magic-missile anyways.
YMMV