Firstly what type of scrubber are you wanting to run? A horisontal or vertical one? I take it it will be horisontal from your description. How will you split the waterflow to go over the scrubber and the DSB?
I dont think it will get rid of the bryopsis to be honest. You have more guts than me for ripping out the DSB of a mature tank. I have toyed with the idea but then said why try and fix something that is seemingly not broken. The risks of livestock losses are just too great for me.