How to handle a big amount of whitelabel sites (with multi-site) For one of our clients we need to setup a whitelabel template. 
I was considering doing this with Craft's Multi site feature which works fine in that way Content management wise.

But, it's probably going to be 50+ whitelabel sites (multi sites) but, I'm afraid this is going to be a mess in the CMS. 

Is there another way to handle this issue or, is this the way to go?
Craft just isn't set up to handle this many sites, as you said it will likely be a hot mess. One way to circumvent could be to create your own plugin to manage things.

Either way I would get in touch with P+T as depending on your use (if every site is a new client) this may be outside of the license agreement.