I've had to do this several times and I found this works well.
Use your formula field and form rule to actually copy a value (your formula that contains the lookup field) into some other text field. Once that text field has a value, you then drive the relationship based on the text field. Then QB doesn't have issues with summaries or other fields.
If form rules aren't an option, (i.e. Grid edit, import). You can use an Action to copy that value over once its created or modified. So it wont be connected right off the bat, but withing seconds of saving the record.
