Am I forbidden from wearing tinted glasses while looking at Facebook as well? After all, they "alter the experience".
Anyway, I think it's silly for Facebook to be going after tools that make users like Facebook more, as long as they don't somehow degrade the experience for others (spamming, etc)
I suspect it has more to do with the fact that many of these tools strip ads.
The correct analogy would be:
Q) Am I forbidden from writing an application using the facebook API that tints/alters the color of the website?
A) Yes, you are forbidden from doing that.
Facebook could be defining anything that blocks or interferes with their advertising and revenue stream as malware.
This is quite unfair to you IMO...downright shameful of facebook to do this.