If you have a heterogenous network, with Windows, Macs, *nix etc then SMB is probably your only real option as it is compatible with just about everything.
With regard to Active Directory, your file protocol selection has little bearing on it unless you're using share permissions and the like, with objects from yourdomain\userAccount
You can of course get away with local permissions in a domain environment - a Microsoft AD installation does not stop you doing that. I am guessing you want to leverage this though, or you wouldn't mention it. So I'm thinking you have a primarily Microsoft infrastructure.
Based on that, I'd aim it like this:
Use NTFS as your underlying file system if you can (I know you've said you're using FreeNAS so that's probably out the window, but I'm just stating it as it's probably best practise for this kind of thing. Personally I'd throw that away and put in a Microsoft Windows Server based file server) - it's very good and you can set the ACLs to use domain\useraccounts, use SMB for the actual sharing protocol and make sure your clients are compatible with this infrastructure, not the other way round.
I may sound biased towards Microsoft here but I don't work for them or anything, it just sounds to me that you are a Microsoft house, with non-microsoft clients. So use the best tool for the job.
In Summary: use SMB! if CPU becomes an issue, get better hardware.