Not sure what to tel you about the theme issues you’re having (I just modified the BP default one), but I get what you mean about the BP groups/forums confusion.
The audience I’m after is used to vbulletin forums, so I actually found some code posted here on BP.org that made groups open onto the group forum by default, and then I put a conditional around the activity stream posting thing on the group activity pages that only allows admins to see/use that. This way, all group activity id funneled into the forums, unless the group admin just feels the need to post something to the activity stream. I also just did away with the ability to post activity stream updates from the sitewide stream page, but you could just modify the ‘post update to’ dropdown menu there to hide and make it post to the user’s profile only.
All in all, I’ve found that Buddypress can be a bit of work if you want to change the way it does certain things, but for most people the features are worth the trade-off of some extra work. I hope you get it all figured out and working the way you’d like