Actually the refusing to flip systems was a strategic decision, not a monetary one. When these blog posts started popping up, describing how the Minmatar were pretty much taking advantage our attempts to play the FW game, many of us were incensed, so we decided to stop playing fairly as that would only line the pockets of our enemies with easy ISK.
Simply put, we could not hold any systems we took so long as a glut of plex farmers existed on the Minmatar side. If the Amarr flipped any system it would be retaken in a matter of days to a week, with the Minmatar profiting all the while. We noticed the pattern and stopped it, resolving to only leave Minmatar systems vulnerable (and therefore not profitable) and defend only 3 systems doggedly: Kamela, Sosala and Sahtogas. This move effectively drove Minmatar plex alts from our warzone - only to have them move to Caldari space and farm those systems endlessly for Minmatar LP.
This tactic was decided upon long before Nulli Secunda announced they would be joining the war. A good number of systems were already vulnerable when this occurred, and our strategy was independent from their arrival. When they did arrive we told them of the strategy and they also began to replicate it in Metropolis. Of course, them being noobish null-bears, they couldn't figure out how to do it right and got their assess whopped every time they tried to fight.
Then came the cash-out, the return of the Minmatar plex-alt swarm, and the mass-exodus of just about every decent PVP group in the Amarr militia. Everyone cashed out, then when there was clearly no chance of ever holding the systems or ever seeing a decent warzone control level again, they said "Screw this hopeless situation, cutting my losses and leaving." I've stopped playing and let my subscription run out since then.
The overall feeling from our side is that the only way to beat the Minmatar as they are is to make FW supremely un-fun for them. No fights, no profit, no nothing. They simply have too many plex alts, too many PVP'ers with heavy assets (now bolstered with limitless supplies of Republic Fleet ships and liquid ISK) and too much of an entrenched edge to ever take down without the resources of a nullsec alliance. Small, unorganized groups do not have the ability to take down the profit cartel built up in the Minmatar militia at this point. The only way to stop plex alts is to perma-camp all entrance gates to the WZ with insta-lockers. The only way to beat a full faction BS fleet is with a better one or caps, neither of which even the more senior Amarr militia members can afford with ease any longer. Even if we could, the Amarr Militia would have to win 10x as often to even the odds, when they already are at a monetary, numerical and firepower disadvantage. This thought crushes the morale of Amarrian militia members and deters anyone but the most cocky PVP noob-group (like Fweddit) from joining and trying to 'help' the situation with smack talk and/or shameless profiteering. So now it seems the only thing left to do is bore everyone to death by being absent and come back later.
Sooo... All that remains now is to translate all of this into an IC perspective!