Saying one is "conflicted" normally means they are confused because they are torn between 2 ideas, choices, etc. Like there is a conflict going on within oneself.
Not really sure what the author of your statement is meaning here, since it's pretty clear he's calling Mueller a Trump hater and nothing else. Doesn't say what else Mueller is conflicted over.
I'm fairly sure the writer, unless an explanation can be given for what he meant, the phrase is not being used correctly.