Sega's [0] main business is pachinko (so gambling). To them Sonic brand being used by fans has very little consequences, if not building most needed goodwill toward their other brands.
Sega was mostly into normal arcade games, and Sammy baught them for their expertise to improve Sammy's much more profitable gambling machines. It's Sammy's CEO that took the lead, and Sonic and console games became a mere side business.
That's where Nintendo is fundamentaly different.
[0] https://en.m.wikipedia.org/wiki/Sega_Sammy_Holdings