I read that, for a network or sites, wordpress impose certain rules in the url generated. is this true? because if is, it could destroy ten years of google indexing in our site… 🙁
Mostly whatever works for your individual sites (I assume they are on WP?) will work for multisite. Only explicit limitation that I remember is following:
While permalinks will continue to work, the main blog (i.e. the first one created) will have an extra entry of blog, making your URLs appear like domain.com/blog/YYYY/MM/POSTNAME. (Codex)
_
Could we managed differents themes for every site in the network?
Yes, absolutely.
And finally, in a networks of site, we could manage the register user in a separated way, or all the user of the net have the same access to the rest of the network?
Users can be handled separately on per-site basis.