I have '88 Hunter 28.5 and I do understand your initial impression, that the boom is too low, but we've had our boat for 8 years, and it's never been a real problem. When we dock the we use the traveler to move the boom over to the port side and tie it down there, out of the way. No problem getting in or out of the cabin. Just a pain when doing the dock duties (putting on/off bumpers, main sail cover, etc.) and having to crawl under the boom on the port side...
As for the jibe, you obviously have to be careful, but It would be above anyone's head (no one would be standing up), should a jibe occur.
The only issue that I've had was when we had a bimini made for the boat, the back stay got in the way, and they couldn't put it too far forward due to the boom height and backstay.
Sir Michael