Saving Intaki from the resource rapesquad at the cost of near bankruptcy has it's advantages.
You know, as far as I'm aware, there's no PF that the Megas actually took off with the resources of any system. According to the news articles I have read, they got really badly burned because they were investing in the systems.
It probably takes pretty substantial capital to start up planetary-scale mining operations, or begin laying down million-square-kilometer-scale agriculture. That is an investment that also includes then taking resources back out of those systems - in fact, getting resources out of those systems is probably why they would invest int eh first place. Not only are the two not mutually exclusive - I would suggest that for most purposes, you cannot have the one (extracting resources of whatever sort) without the other (investing in the things that extract resources, whether literal mining facilities, or factories, or infrastructure).
As far as Ishukone goes, it just makes good sense for them - politically it is going to strengthen their position, because it may swing some of the in-between corporations to their side. It would be surprising if SuVee and NOH for example wanted to spend the money to help KK fight the Federation when they could be selling Federal citizens protein delicacies and specialty Caldari porn instead. Plus, Ishukone has more foreign exposure than most of the others, it seems, so they benefit from things not devolving into all-out war. And if they reach some kind of acceptable compromise on Caldari Prime, it makes them look good, and makes Heth look like an asshole.