First: I think calling the Muslim Brotherhood terrorists is a terrible idea. I'm just thinking about the language here.
Second: Terrorism is by definition something that other people do, like rioting. No one ever comes up to you and says "I'm a rioter!", or "we are planning a riot" it's something that gets called by others. Even groups like Al Qaeda claim that it is the US that is the real terrorist, implying that they themselves reject the label. So terrorist is inherently a loaded term. "Acts of terrorism" is less so, but only because it exists as a legal definition (i.e. that terrorism is itself something you can be charged with, so it directly refers to something specific). That definition favors the government, but it also the only one we have that is agreed upon (which is why PTTG?? is using it above: it has an actual definition that allows you to do things like collect statistics). This is a similarish situation with the word "Genocide": rarely will you hear someone proudly proclaim their support of genocide, and often will you hear someone accuse someone else of it (even those weirdo white-supremacists on the internet use the phrase "white genocide" to make their point, which means that they realize that genocide has negative connotations), but genocide nonetheless has a definition that is verifiable and corresponds to objective facts on the ground (i.e. the targetting of a specific group for destruction), so the term is still useful, but you must be careful with it because of that difficulty.
Third: By contrast, "terror" is something anyone (well, anyone with guns and bombs) can do. And unlike terrorism, you might willingly use the word "terror" to describe your actions. You might say that terror is part of your strategy (although you wouldn't usually say this to the press, obviously), as such with the terrorbombing in WW2. Terror thus has a meaning that is distinct from terrorism, although closely related. Consider: you mention deathsquads. That doesn't sound like any definition of terrorism I've ever heard of. In particular, that sounds like some sort of genocide or political equivalent (i.e. killing of dissidents). Going around killing people extralegally, even for political purposes, is not by itself terrorism! It's certainly using terror, but the distinction is relevant.
Fourth: You might say "who cares?" Fair question. This is where I point back to my second point: No one thinks they are a terrorist or do terrorist things, and the only definition of terrorism that is objective immediately favors one side (i.e. the US and governments, and by that definition governments cannot use terrorism); by contrast, people are willing to admit that they are, for example, insurgents, or rebels, or using terror to break a groups will (again, terror-bombing). So using it at all except in the legal definition of it just means you are essentially joining one side rhetorically over the other, i.e "The US/ISIS/Israel/Russians/Ukrainians/Chechens/Syrians/Iranians/Saudis are the real terrorist, not us, we are counter-terrorists/freedom-fighters!" And if you try calling them all terrorists, then it just comes off as pointless moralizing by people assured of their own moral standing (by contrast, since terror is used neutrally, even if you think it's abhorrent and categorically unacceptable, it's still a neutral term).
Using the word "terror" sounds like it makes no difference, but it makes discussion clearer. Call the US terrorists and you will always invite arguments, because terrorists are by definition "the evil guys." Not just the bad guys, the evil guys; the heartless monsters who kill for no real reason because they are just so evil (you may not intend it like that, but we can't ignore the sixteen years of rhetoric since 9/11 saying exactly that). But "terror" does not have that problem, which means it's a much better word choice. And if you want more specific points, you use more specific words, like "insurgency", or "state terror" or "mobile killing squads" or whatever it is (behold the richness of language in describing violence). And yes, I know this distinction isn't respected elsewhere, but why do we have to follow their rhetorical rules?
tl;dr: The phrase "State Terror" will always cause fewer arguments over definition and semantics than the phrase "State Terrorism", and we already have enough arguments as is. Everyone will still know what you mean if you use one phrase over the other (or even interchangably), but one of them causes fewer arguments. As an aside, the phrase "State-
Terrorism" has a completely different meaning from either, even though it is also used interchangably.