I don't think the durability thing was a huge issue for either player at the time. IMO, it came down to how much Sides was going to sign for and what he was going to give you, versus what it would cost to sign JB55 and what he was going to give you, plain and simple.
Sides deal kicked in at the age of 33 (signed extension when he was 32) for 4 years at $4m, which was only a $750k raise after some very good play for the B's. Boychuk turned 30 his last year in Boston and was going to be 32 during the season his new deal would kick in. The B's had to have an idea of what JB55 was going to cost to keep? Let's say it was $5.5m over 6 years. That would mean that they would have their Top 3 D all 32 or older, all on long term deals for relatively large $$$ (roughly $15m per).
Both Sides and JB55 played a strong defensive game, with JB55 having a better shot and giving you a little more offense (not a lot). Sides was good for 15-20 points, JB55 20-25. I believe that when Sides agreed to that $4m deal, the B's pretty much made up their minds that he was their guy based on the value of the deal (remember this was pre-injury). It was definitely debatable at the time over which D they should keep, but I don't think it was a bad decision. In hindsight it's easy to second guess the deal because of Side's knee issue, but the B's didn't have a crystal ball.
I liked JB55 quite a bit, but IMO the Isles drastically overpaid him. They gave a guy that was going to be 32 in the first year of a deal a 7 year contract worth $6m per (based on several good years with the B's and one very good year with them). Last year, JB55 looked very average and the Isles are on the hook for six more years and $36m, while the B's had to buy out Side's last two years. The silver lining was that the B's appeared to have drafted two very good D-men with the picks they acquired for JB55.