Create a network of sites

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)

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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.