I would love to see this kind of merger, but I don't think it ever happen. Sega is probably too big for Nintendo to really want to take a bit into, but more importantly, you have to look at what the talent wants.
There was a rumour a few days ago that was generated from a misinterpetation of an interview with Yuji Naka about the furture of Sega, Most people took it as Sega actually working on new hardware, but that wasn't what he said. Basically, he said that his team is working hard to help push Sega out of their problems with the hope that they will become strong enough to go back to hardware.
While Naka can't be unfairly singled out as the voice of Sega, I wouldn't be surprise if this was not the generally sentiment, at least among the old gaurd like Yu Suzuki. Just as that EA rep said that Nintendo has hardware in their DNA, I think Sega is also like that, maybe moreso because of their arcade centric business.
That might explain why the employees were pushing for Namco. Namco said that they were willing to be absorbed through management and name. They were willing to give up their NAME! I don't know what their finacial situation is, but certainly a partnership with them would have been the most acceptable in terms of independence. A merger with someone such as Nintendo and Microsoft would essentially destroyed the chance of getting back to hardware in the immediate future.
If Sega, however, was to finally go belly up, I would hope that Nintendo would be there to at least get Sonic Team, AV, and maybe Overworks personel. But until that happens, assume that Sega would actually like to make system again, which would be a better dream for me than them being partnered with Nintendo.