Eren also knew that her abilities weren't something that he needed. Although they could be useful in certain situations, they mainly overlapped what Yelen could already achieve.
Moreover, he didn't have time to strengthen her ability. Unlike other abilities that could strengthen on their own the more one used them, Ghost Queen's ability was different. It needed a lot of work to be put in.
Moreover, it was also true that Mist was a bigger threat for now. Even though Eldric was there to keep her busy now, the more cards there were, the better.
In any case, Ghost Queen couldn't defeat Mist even if she tried. It was at best a minor annoyance for Mist.
For him, Ghost Queen was more useful alive than she was dead. Until now, it was Mist sending people undercover to destabilize other places. Ghost Queen gave Eren an opportunity to do the same.
Despite agreeing with the Ghost Queen, Eren couldn't outright agree with her.