I’m having this exact same issue.
A couple hours of research on pre_get_post hasn’t given me a solution yet.
I haven’t seen any code examples, but according to the Codex it might be solved by adding something like this to your acf_relationship_query query $args:
$args['fields'] = 'post_title';
This might not remove the existing filters, however. I’ve emailed ACF for support on this issue.