Pointing out a legitimate fucking motive for why they might do this, isn't "using trans rights to protect a cis man". It's just explaining one of the reasons why people find this particular source insufficient.
It's one of many red flags.
The church is not gay it marries gay people. So homophobes hate the church. That's not using gay rights to protect the church, its pointing out why they might be doing the thing and that doesn't mean the church is necessarily good either.