If someone beats someone up then of course they need to be punished. Their motives for doing so aren't really the issue - they committed a crime.
The difficulty arises when we start changing the scope of what is considered a crime - and what 'transphobia' can get defined as. For my money, I think the affix of -phobia to things that aren't actual psychological fears which no one is responsible for has always been a silly thing to do.
I use the word 'homophobia' occasionally, but I really don't think it's a good term, largely because you just end up with endless dull posts about the definition of a phobia which deflects from the fact that what we are talking about is simple unfounded dislike, prejudice and discrimination against certain people. I understand why the term caught on, but I think it's a silly, lazy jargon word.
And, that being the case, it's started a trend for copycat etymology, with 'transphobia', 'islamophobia' and even 'christophobia' springing up.
And the problem with jargon words is that no one has a specific definition of what they mean. We understand what racism and racial hatred is. It's very clearly dislike, prejudice and discrimination against people of a different colour skin or culture.
It is entirely unclear, given the myriad of 'microaggressions' that come under the catch all banner of 'transphobia', what it constitutes. So what are you being threatened with jail time for? Assaulting someone? Of course, no question.
Calling someone the 'wrong' pronoun? Objecting to a male on an all-woman shortlist, or a female sporting competition? Not adopting an unquestioning affirmation approach to a child who believes themselves to be the opposite sex to that which their body shows them to be? Being a lesbian and saying no to a penis? Really, where is the line being drawn here?
Crimes like assault, murder, rape etc. are already illegal and if someone does those things, their reasons are useful for providing evidence of motive, but they neither add not detract from the nature of the crime which should be disgusting enough to a decent person without needing to add an extra layer of frisson.
But thought crimes are the stuff of science fiction and need to stay that way.