The details that one can infer from the petition and the text attached to it don't look pretty. All in all, this looks not so much a desperate last resort measure as an attempt to "manage" science, based on the University management's understanding or views on what is and isn't good mathematics. I do not think I can offer much practical advice on top of the excellent suggestions, which I would like to second:
Don't let them hush this up. Instead make sure the story widely known to the scientific community (to an extent I believe you've done this already) and the general public at large.
See if there are any prominent applied mathematicians who would be prepared to send a letter to the University management and the NWO expressing their concern and stating that an attempt to handle the situation in this way has already damaged the VU's reputation and the damage will be far worse still if the intended measures are carried out, making it clear, if possible, that if the management sticks with those plans, then from some moment on, if someone is introduced to an analyst from Amsterdam, the reaction of quite a few people from both pure and applied (inadvertently, I'm sure) would be something like "you're an analyst from Amsterdam.. I see..".
However I would also like to make a possibly controversial point. I think one should refrain from promoting algebraic topology or another area of pure maths to the general public by saying "look, it is useful, because ...", and then mentioning an application or two. By doing so one subscribes to the idea that algebraic topology is there only to generate practical applications. And I think it is this idea that is the source of the problem.