What about races? You get dropped dab smack in the middle of the game without any kind of information as to whom you're supposed(or not) to invade. Just a while ago, I ran a penitent chapter, and cleared out all orks form the map. There were no Tyranids or Chaos to be seen, so all (I think) I could do was wait for the inquisition to get pissed.
Is that just a sign of rickety jury-riggedness of the game, or did I miss something?
As said before early alpha is a source for a lot of the issues, but in regards to whom you're supposed to invade...
In short, humans in Warhammer 40k are space fascists worshiping the decaying corpse of the god-Emperor, with the Space Marines being (in their ideals, at least) the most prejudiced and violent of all. From a game perspective, the "ideal" space marine chapter would probably see the various factions thusly:
First, the various types of humans:
Imperium: the great unwashed masses of humans. Unlike SPACE MARINES, they're pretty normal (well, unless they've mutated or something). PDF (Planetary Defense Forces) and the Imperial Guard are, respectively, the militia and general military of the humans. On an individual basis magnitudes weaker than a space marine, but there are magnitudes upon magnitudes more of them. Some space marine chapters want to protect them, others couldn't care less about them.
Mechanicus: the machine-worshippers. Mars is effectively their homeworld. They also may or may not worship mecha-cthulhu, but officially they are fellow emperor-worshiping humans and part of the Imperium. They also happen to be the general custodians of technology, so try to stay on their good side.
Inquisition: the human inquisition. If you love the emperor and purge enemies of mankind, stay in their good graces. They're the religious space-spies of the Imperium.
Ecclesiarchy: the Church part of the great religious space fascism. Technically "no man" may hold arms directly under their command, so their military is all-woman. Fellow humans and part of the Imperium.
Heretics: deviants. For in game purposes this is pretty much always the very dangerous kind of heretic-- worshippers of chaos. Think evil demons, with various chaos gods representing various aspects of sin/evil. Many humans and SPACE MARINES have turned to the heretical ways and now serve chaos. Not all strictly human, of course, but many of them once were.
Next, the horrible xenos-- anyone not human is impure and a threat to humanity:
Eldar: Space Elves. Back in the day they partied so hard they spawned a god of chaos. Nowadays they are relatively few in number but advanced in tech. Also work in mysterious ways, blah blah blah. Not "evil" in the traditional sense but still filthy xenos.
Orks: They're orcs. Yeah. British hooligan orcs that are probably a genetically-engineered weapon from bygone days. They live to fight and fight to live, etc etc. Their tech is more or less scrap junk that functions based on the power of magic space-belief.
Tau: The Federation (and possibly all mind-controlled). They're actually a collection of various races, led by the Tau, that serve "the greater good." Not "evil" in the traditional sense but still filthy xenos-- even the humans now on their side. If I recall correctly they were originally introduced as "the good guys," but were later adjusted to be more grimdark and match the rest of the universe, so possible mind-control.
Tyranids: basically the Zerg (of course Tyranids predate Zerg, but I doubt Tyranids were the first to do this either). No diplomacy option for them since they only exist to feed.
Necron: Space Robot Mummies. The Evil kind. Probably the most dangerous of all. Most are scattered in tombs across the cosmos, waiting to awake and more or less end the universe. Generally speaking probably the only faction you want to heavily outnumber as a space marine.
As the diplomacy screen would suggest, just because many of these factions are filthy xenos doesn't mean humanity
always kills them on site. Sometimes assistance and temporary ceasefires/alliances help combat even greater threats. Of course, the fact that "tolerant" is a disadvantage should suggest how the Imperium/Inquisition/Emperor feel about xenos.
Edit: I should emphasize that these are merely the 'ideals' for the space marines. You can consort with xenos and cavort with chaos if you want, but your fellow humans will likely not be pleased, possibly to the point of trying to kill you.