Only weird bugs would make one miss that warning. You get the warning from orc town leaders (or sometimes named black mages in the case of the Hashishin). And you can always avoid getting the second warning by not talking to any leaders after getting the first.
As for the second question I dont know, but I think you could do that. You can definitely do all quests that dont require talking to the local head honcho, initialize liberation by attacking him from outside talking distance (a spell or an arrow will do nicely), kill him in any way you please (he wont talk if pissed at you) to make sure he wont run away with any essential items, and then either stay to duke it out or teleport to the outskirts of town and take on the orcs one by one. Ditto for Hashishin, but you wont be able to get into Ishtar peacefully if you play this way. A mild spoiler is that Trelis and Mora Sul are the towns where you'll want to talk to everyone. You could also make sure to do those two cities early in your career, and then just accept that orcs/hashishin attack you on sight at other locations. The latter would perhaps make roleplaying sense, but you'll miss out on some hints about whats going on in the world that way.
I'm fairly convinced that the rumour that is floating around that orc/hashishin hostility is triggered by liberating a fixed number of cities is false. A lot of people seem to believe that it is unsafe to liberate more than 3 orc cities, but I liberated all in my previous game without getting attacked on sight anywhere. The unsafe behaviour is rather to liberate 3 or more, talk to a leader to get a warning, liberate one or more beyond that, and talk to another leader to get the second "warning".
Another interesting observation is that both successful liberation and "liberation attack" (when the entire town comes for you) seem to be triggered by the total number of deaths in a city at the time when you make your first kill. I lead sandcrawlers into Bakaresh and made them kill about half the garrison of the temple there, after which it was enough for me to murder one Hashishin to get the "someone is murdering our people" warning, and one more to start liberation. Both murder victims were well out of sight. Without external "help" I think you need more murders to start liberation. At any rate it seems certain that the total death count determines whether liberation is successful, as killing about five of them was enough to set the city free.
MORE EXPLICIT SPOILERS: I've observed two ways of breaking the main quest through liberation quests. Namely letting people with keys in Mora Sul (particularly Gonzales who you need 75% to get to) or the Trelis orc leader run away. It also used to be possible to make the Shaman holding the essential ancestor stone in Nordmar run away, but I didnt notice "liberation behaviour" by that particular orc camp after the patch. Both can be avoided by doing all the quests in the respective cities, but if you like me end up without enough rep to get to Gonzales (quite possible as the MS quests branch) you can solve it by simply running in there and kill him first of all... Then you can teleport to the outskirts of town and pick of enemies as they come for you one at a time.
I think PB should make it necessary to kill the NPCs holding essential items in order to achieve victory in those cities. General scripts for liberation and such probably saved them quite a bit of development time, but they should have put in a few exceptions in order to ensure consistency of the game. It would suck to have to restart at level 40 because a main quest item is gone.
