Can we please dispense with the fallacy that the LTD is some sort of huge cash cow for SE? If that was actually the case, then they've been leaving millions on the table for the past three decades by featuring 0 love triangles in subsequent mainline Final Fantasy games.
The reality is, FF7 features two of the most popular heroines in the entire series, and yes, they're going to market both next to the most popular protagonist of the series at times.
I don't know if they care that much about shippers, per se, but they certainly care about keeping both Tifa and Aerith fans happy (obviously there's a lot of overlap) so they keep buying their merch. Aerith's role is what it's always been - the Cetra who gives her life to save the planet. So in what universe is undermining and retconning Tifa's role in part 3 so that she actually does become nothing more than a fanservice character a financially responsible one?
I doubt SE's recent financial woes will have much of an impact on part 3's story at all, but if anything, it would incentivize them to be more conservative in their storytelling and hew closer to the OG. If Part 3 ends up feeling like a huge middle finger to fans of the OG, how many of them do you think are going to be lining up to buy the inevitable remakes of FFVIII, FFIX, FFX, etc.?
Bad quarters mean two things: 1) layoffs, 2) less risk, not more.