Despite both ending up with TikTok staying up in the US, having the ban be unconstitutional or not exist at all is different from having the ban in place and a deal to avoid it. What the ACLU was fighting for would have removed leverage from the government/president.
Technically, and unfortunately, yes. They are a single-issue organization, and that single issue takes precedence over any other consideration. I doubt many of them who are involved are happy about him being able to use this to consolidate, but there are always external effects when you have a single major priority (especially if it's a good one).
https://action.aclu.org/send-message/tell-congress-no-tiktok... https://www.aclu.org/news/national-security/banning-tiktok-i...