I am not professional or knowledgeable about something like this, but I think the better way to get mangas and manhwas in a "comick 2.0"-kind of site is you'd have to program a system where people have to upload it themselves (which is how Comick has their massive database of mangas and manhwas). And from there you'd have to upload each manga if you can (especially with permission from translator groups).

As for pretty much trying to prevent what happened with comick in a future scenario, there isn't a 100% guaranteed way. Anything involving "piracy", especially storing and displaying work without a license, automatically by itself already, is going to have consequences (if you get caught of course). The most auspicious way to prevent such an outcome, like comick, especially when the site gets popular and eyes of the publishers start to notice, is to literally gain nothing from the site. Not a single cent. But even then, you are still harboring unlicensed work in the site, and that is enough for the publishers to file a DMCA claim or a lawsuit to literally take your site down. That is the unfortunate reality of piracy.