How much freedom Slott did or did not have is a no-point.
Slott is a writer. As such, his job is to write. If he has no guidelines, great. Good for him. He can write about Spider-man getting butt-probed by aliens if he wants. Wonderful. If he has guidelines, great. Good for him. His job is probably a tad easier now, given that he has some confined space to work in, and he still has a grotesque amount of freedom, but for some points to anchor him.
Slott is a writer. As such, his job is to write. Assuming that he is professional (I don't know him personally, so who am I to say one way or the other?), regardless of whether he likes what confines him or not, his job is to create the best story - or "logic," as he writes in the link you provided - he can with the groundwork already provided. If the story he created is horrible, then he did not do a very good job. If this was because he could not work within the groundwork already provided, then the professional thing would have been to step away from the project and let someone else handle it.
Being that he does not seem displeased with his work on the project, I'm assuming he wrote a story that he felt was worth seeing the light of day. As such, I can't figure out what you're griping about. Please provide me with a link in which Slott complains up a storm about the confines of the project and how it prevented him from writing something good.
Also, you mention Activision. Activision is a publisher: as such, Activision has nothing to do with the writing of their games. Slott - again, in the link you provided - accurately identifies Beenox as the game developer. Thus, if you feel the need to blame someone about it, blame the fellows at Beenox. And/or Slott.