Hi Pierre! I understand your dilemma perfectly well.
So, do we have to conclude that Mediawiki isn't a good choice for an enterprise (with these requierements) ???
Essencialy, yeah, MediaWiki sucks for the situations where you have sensitive data stored on your pages and possible attackers.
And no money for paid wikis (Confluence and cie).
Well that's weird. You've described that the wiki will be used in such a big scale... it seems to be pretty important project to spend several thousand bucks (=salary of 1-3 employees for month) on it and buy the TWiki or Confluence license.
For MediaWiki I can recommend IntraACL as well, but you have to be sure that there is no potential attackers in your case.
Just to note, we have a setup consisting of several wikis as well; and we have automatic replication set up between them (through import/export and configs/maintenance/replicate.php script); and in each separate wiki there are many projects which sometimes have (and sometimes don't have) different access rights.
But 100+ different customers isn't our case... so it's simpler for us. An idea is to use a namespace for each customer for the isolation :) it would be very simple for users and I think the isolation would be strict enough with IntraACL. The problem would be the File namespace, but there's NSFileRepo extension... it allows to use more than one namespace for files. But of course it should be checked first.
Also, about the dilemma - I would still recommend MediaWiki, and it's not the performance on big databases which matters, but the extensibility.