Do I need a comma before "in that"?

The petitioner is filing against the respondent for custody of the subject child in that temporary custody shall be with the petitioner and the respondent's rights of visitation shall be suspended.

Do I need a comma before "in that"?

It does need a comma. Without the comma, the "in" becomes a preposition and the "that" becomes an article. SO it reads as if the child is in that custody, like "the pen is in that box".

Instead the intent is that "in that" is used in an explanatory sense, so the comma is, I feel, important.

Without it the sentence reads that it is talking about the respondent, not the child: the respondent...shall be with the petitioner.