So oddly enough, lots of places do not seem to check for ROOM_NO_MAGIC where they really ought to. I didn't keep a running list, but from memory:

In handler.c, in the function can_astral( ) there's no check for victim's room being ROOM_NO_MAGIC. That seems wrong.

In magic.c, in quite a few places, there are checks for ROOM_NO_ASTRAL but no consideration for ROOM_NO_MAGIC.

To each his own on the latter, just do a search for ROOM_NO_ASTRAL and add NO_MAGIC as you see fit. Personally I don't think you should be allowed to teleport randomly into non-magical rooms, nor do I think any sort of astral travel spells should work in non-magic rooms. My view is that ROOM_NO_MAGIC should mean everything, including astral travel. Whether the devs had a different opinion or this is just an oversight, who knows. I consider it a bug, so there you go.

Bonus Points: If you've installed the snippet for rune transportation, or something similar, it's probably a good bet that it doesn't check for ROOM_NO_MAGIC either.