For high speed ejections we always have to look at the equivalent airspeed (EAS). That's what basically matters for wind blast. (Although I guess there are heating effects which might not relate directly to EAS - I don't know my high speed aerodynamics.)
So if SS2 were doing Mach 1.0 at say 50,000', the EAS would be only 250 kts. Rough but nothing like ejecting at Mach 1 at sea level, with an EAS of 660 kts!
(It can also be remarked about ejection stories is that it can be hard to tell what the actual speed was at the moment of ejection, which might sometimes be slower than at the moment the pilot last had a chance to look at the gauges.)
I'd just guess Siebold was lucky to not have sustained much injury during the breakup, and despite loss of consciousness from hypoxia, and happened to wake up sufficiently to unlatch the seat belt at some lower altitude and pull. One news article I saw suggested he was just in his seat with little structure around, but I'm unsure about how accurate the article might be.