I normally choose a custom game with aggressive AI and sometimes raging barbs. My question is whether i have to enable permanent alliances, to make the mercurians work right? Will the permanent alliance with their summoner even be active if the option isn't checked?

No need to have the option enabled, you'll have a permanent alliance with Basi either way.

I think that there are problems if you manage to get a permanent alliance before you build the Mercurian gate, so it might be safer not to check this option.