And that's where you would be wrong. If they had prior contact with the Vipers, they would've known about their religious fanaticism and that their weapons are tipped in poison. From what is said in the lore, they knew about neither of these things. So the idea that there was some kind of treaty between the BOS and Vipers is without a doubt, false.
... actually, please go read the lore for the BOS, because my statement is completely based on the lore. Lore shows the only times the BOS has ever gone after someone is because they have technology they want, or because that group is openly hostile too them. Case in point, the BOS started their war with the NCR because they wanted too take away their tech; where as the Master's super mutant army was going out of it's way to capture and turn as many humans as possible into super mutants... which would've eventually included BOS personnel.
Actually, in Fallout 1, we see the Brotherhood having something along the lines of a diplomatic representative at the Hub. After they defeated the Vipers in 2155, they sent scouts to the Hub and other locations to make connections in their hunt for the surviving Vipers who fled north and east into the Sierra Madre Mountains.
In Fallout 2 they're investigating the Enclave because they have major tech advantage over them. What was the BOS's mission? To gather and maintain technology! What did the Enclave have? Technology! So my "assumptions" are based on BOS actions listed in lore.
*Sigh* I'm not twisting anything. Or did the power armored soldiers only have melee weapons and couldn't fire back? Sorry Okie, but if you were a soldier wearing power armor who was guarding civilians, and some nuts started firing at the civilians you were guarding, are you just going too sit there and watch? Or are you going to return fire? That's just common sense... and if you ask any person with military experience, that would be considered an engagement between the raiders and the soldiers in power armor.
The game examples are based on LORE. And no, actually, in lore, the majority of raiders are presented as power hungry psychos or drug addicts living day to day to sate whatever gets them off, be it drugs or violence... or both. Are there some organizations deemed as "raiders" who don't fit this? Yeah, like the Great Khans in Fallout New Vegas until the arrival of the NCR and what happened at Bitter Springs.
Yeah... except their only point in living to see tomorrow is to cause "anarchy and chaos." Which sorta tells us that they really don't have much much of a sense of self preservation, because people who have that, don't go about killing pretty much everyone "weaker than them" if they don't have too. People who have a sense of self preservation also tend to try to make a life, be it farming, ranching, scavenging, trading, merc work, etc. etc.. So yeah, the lore contradicts the OP and your argument that the vast majority of raiders are anything but suicidal psychos with little to no sense of self preservation.