We actually use a somewhat similar setup in Fury and it's worked pretty well for us. In the effort of sharing the little knowledge I have with the world...here goes!
We started off as a sky only shell but the idea was to gear people enough to expand into other endgame activities. There is no point system or attendance tracking. We have two mandatory times which usually end up being either farming or gods/jailors. However we have used this time in the past for Einherjar, KS99s, HNMs etc. The idea was exactly what you said...not everyone can devote 40 hours a week to the game. Since a points system will inevitably favor those people that can play more often, we shy away from that.
I won't lie to you, it's not always easy. We tried to run an completely internal Dynamis shell for a few months but it simply didn't work out. Since it was being run on a non-mandatory day, it was difficult to get the numbers that we needed to really give each zone a legitimate shot. We did, however, manage to get wins in all main cities and Beaucedine with numbers around 20. We also run Salvage, Einherjar and Limbus internally but it's all optional. Some days we don't have enough to run. Some days we have more than enough.
It's not the best system for everything but it does work for us. It sounds like you're wanting to focus more on HNMs than we choose to but that's a byproduct of our system. The more lax you make your rules, the harder it is to be successful initially at some of that stuff. Ultimately it comes down to your members developing a sense of camaraderie and wanting to accomplish things as a group moreso than for themselves. It's a lot of fun seeing friends get an item that they've worked for but getting your membership base to that point may take a little time.
Anyway, hopefully this helps a little bit. We're far from perfect but it does work for us. If you'd like to talk any more about it, you can PM me here or shoot me a /tell in game. In any event, good luck with the ls!