I don't think it's all about their "relationship". Having read some of Ashley's posts on other forums, I get the sense that it's deprecated because of Scirra's new philosophy with this tool: They want to stick to real browser wrappers only. CocoonJS Canvas+ isn't a browser wrapper; it's a specialized environment made for HTML-5 games, and so it has a non-standard way of implementing certain functionality.
Since Construct 2 is made to work with standard browsers, to officially support Canvas+ would mean having to maintain a separate batch of workarounds just to get things to work within it. And if they go this route (which they already tried), if Ludei decides to change something in their framework and it doesn't get clearly/accurately communicated to Scirra, there will be a bunch of angry users complaining that Canvas+ support is broken in Construct 2.
So Scirra gets the blame, and it affects people's impression of the product and the company. This is why Ashley has deprecated it, and this is why he is deprecating all export options that are non-standard, because all of them carry this risk. By choosing to focus on wrappers that support the standard browser protocol, Ashley can be sure that if he's got it to work in a browser, it should work in these wrappers, which promise to follow the same protocol rather than inventing their own.
That said, CocoonJS Canvas+ is still the best option to export for mobile. The fact that it's non-browser is what allows games to run so performantly through it. I think it was a worthy tradeoff, and as sad as I am that there is no longer an "official" export option, I think I can understand Ashley's reasoning.