I thought I'd give it a try, but it seems even a fully equipped medbay can't supply the Engi medical dispersal with enough little medbots to keep a crew alive without oxygen. So much for that anti-boarding strategy. I'll have to rely on proper micromanagement.
In fact, I just looked the matter up and found out why not. According to ftlwiki.com: So there you go.

Now, on the other hand, since the healing rate never improves outside the medbay, you could get away with only medbots for short travel through constantly evacuated sections of ship. This would still mean most places your enemies board would result in asphyxiation, and unlike on most craft it wouldn't leave your auxiliary crew any the worse for wear. Sound feasible?

Possibly. The amount of health you lose for just passing through an area without oxygen (if you don't stop) isn't much, so I imagine your guys would be healed shortly after arriving back in an oxygenated room.

It's an interesting idea, as boarders tend to board rooms at random, so they may well start off in a room without oxygen.

Whether or not this is easier/safer than simply draining the oxygen from the rooms as needed (i.e. as per normal) is what you'd have to test...

This.

You would still want to upgrade doors early unless you were planning on fighting them in the vacuum. You would likely want to upgrade O2 as well. If most of the atmosphere is already vented and the O2 takes a hit you start being in trouble a lot sooner, i.e. beginning the battle with < 40% O2. With that being said, I haven't actually tried it.