Not just Comixology, it was extremely bad planning from both them and Marvel. The timeframe was much too narrow and it was publicised in mainstream media meaning many more people than normal tried to jump on it.
I think I managed to grab 30-40 or so comics. Some are newish that I've considered recently, others are older comics that I've recently put in one of the 15 or so boxes I've just shoved in my loft - saves me having to dig them out!
I'm no expert, but you'd have thought they could have at least moved all the issues that were in the Marvel promotion over to a separate (temporary / bigger) server.
That way, even if the promotional content got swamped and went down, at least the rest of their material stays accessible and those not taking part in the promotion don't notice any drop in service.
Apparently, even the DC digital store (which is just a front-end for the DC content available on Comixology) experienced some slow down because of all this.