You may be right but, if there is no longer a tie-up between Alliance and Qantas, the whole E190 wet-lease is much more transactional for QF and much more vulnerable to being replaced by an enlarged A220 rollout within one of the subsidiaries Qantas already controls.
I think you might be overthinking this slightly. First, the E190 contract was agreed before Qantas commenced their takeover bid. They had a 19% stake but no representation on the board, Alliance perused that commercial opportunity entirely independent of Qantas’ strategic interests.
The fact Alliance isn’t an owned entity isn’t particularly relevant IMHO. National Jet wasn’t until 2020 either. The franchise agreement will stipulate minimum standards for everything from maintenance to the brand of paper napkin used, and Qantas have complete control over scheduling etc. Other than assuming the capex (such as it is) and overheads, Qantas doesn’t gain much by owning Alliance (regarding the E190s specifically, the entire business is a different discussion). If Alliance fails to maintain the requirements of the Qantas franchise agreement, you can be sure that Qantas will be entitled to financial compensation and/or terminate the agreement.
I wouldn’t be too certain about the E190s being retired from Qantas service as soon as the A220s arrive. Alliance purchased them for fire sale prices and there is no way that the A220 fleet will compete on capex costs (of course operating costs should be lower). If you look at how the 717s are used, they have relatively low utilisation for much of the year but flex up significantly during peak time. You can’t do that with new aircraft, they need to be earning revenue all the time. With the low cost of the E190s, it would likely make a lot of sense to keep them as that flex fleet. Retiring the 717s quickly also has the benefit of retraining NJS’ pilot group onto the A220, rather than having to hire off the street during a pilot shortage to add the A220 while initially keeping the 717s flying. Keeping Alliance flying during the transition period should be a bit easier to manage.