clearly if you provide someone a piece of GPL software (such as a perl script to do something useful on their server) it's GPL so it's free software and it's already source code.
The point is that the Affero clause is very clearly targets software that is being used over a network connection rather than being distributed.
It is not possible in the least that the "semantics of the communication are intimate enough" to qualify -- the semantics of the communication are HTTP, an open standard used for extremely varied purposes.
I'm quite sure the MySQL guys are simply wrong on that, but even if they're not, it's clearly not the case for HTTP.