The difference isn't paying upfront or at the end of each week. The major difference is that paying clans to join, leads to leaders making random weak sides who play just for money and creates an extremely toxic fake competition in-game (i.e. l2 dex, e-global, valhalla and this kind of servers). Paying clans just to join absolutely kills the rivalry between them as there are no real losers and winners. Everyone gets paid at the end of every week so who cares right ?
Rewarding the winners with cash gives a massive motive to the leaders to create strong sides and try their best to win without giving any advantage to any clan (unlike paying people to join and basically giving them free premiums and whatnot). In this case, there will always be losers and winners and the rivalry will be kept alive.
I hope that clears up the massive difference between the 2 scenarios. Look at all those big russian servers. No1 makes fraps flaming about which side is better. Everyone cares about daily 9v9s or organized ones. There is no clan identity anymore because leaders simply don't care. They have been so detached from the clan's identity that most of the times the leader's CP holds a different name to the side's. This is a very important point to think about.