Should we not call someone who rapes a rapist, because it's "not nice"? Wowie.
Homophobic/transphobic are descriptor words for the actions someone chooses to take and exude upon other people and should not be flagged as violating the "Be nice" policy unless directly harassing another member of the site (which you have not included examples for, so I'm assuming you just mean any reference to such language should be removed from the site). We would only be invalidating the victim of these oppressive occurrences by censoring language to accurately describe an oppressor.
If an OP calls someone "homophobic" for belittling them for their personal life, maybe the real person in violation of "being nice" is the person exuding their negative attitude onto them in the first place.
"An opinion is whether or not pineapple belongs on pizza. When we invalidate someone’s gender, mistreat same-sex couples or fight against inclusive policies, that’s oppression. Big difference." - source
Addendum, now that it's actually clear what your question/problem is: It seems your underlying issue is with grammar and has nothing to do with this site. You are heavily focusing on what "phobia" means without allowing room for the true definition/context of "homophobia".
Homophobia definition:
"dislike of or prejudice against homosexual people."
We are not here to parse apart language and debate whether the composition of any word should be changed to better fit it's definition in the English language (or vice versa). You can choose to reject the true definition of this word based on the definition of its suffix if you so choose, but asking everyone else to do so is quite frankly an overzealous notion that is belittling to the people who value this word for it's ability to speak to the injustice against them.
So again... No thanks.