Because a strong attack destroy a thing doesn't mean a weaker attack won't as well. The Shinsuusenju has more than thousand arms. It's in terms of numbers that these Bijuudamas were needed to reduce all them to pieces. I'm questioning the durability of the jutsu here
I think 3rd raikage could possibly outlast the shinsuusenju. Its a sage mode technique and we know that hashirama doesn't have a permanent sage mode after 5 - 10 mins he should run out of sage chakra which would deactivate shinnsuusenju. All third raikage has to do is not get hit and use his hell stabs to eliminate arms.
Honestly, third raikage isn't getting put down by shinnsuusenju. He tanked a tailed beast bomb. You can capture the 3rd simply kill him in a battle.