None of those developers died from going high budget or from abandoning their original audience. SK, Factor 5 and Free Radical all continued to make similar games to what they were known for; its just that they all sucked. But even then that is not what killed those studios. Hell, SK apparently even got full reimbursement for Too Human from Microsoft! What killed each of those was publishers pulling out of publishing deals with them (Brash killed Factor 5, the loss of Star Wars Battlefront III killed Free Radical, and numerous gaming deals + the lawsuit + Nintendo pulling out of ED2 killed Silicon Knights). And again, Free radical is a horrible example: Their games did equally good on all platforms. There is no connection between them and Nintendo, let alone "Nintendo management".
And Sega is a horrible example. For one, whats keeping the company afloat is Sammy not Sonic Wii/DS games. Sega's problem right now is that their division (particularly the overseas offices) are drawing too much red ink for Sammy's liking. And Sega's losses and gains were never platform specific. They had bombs on the HD platforms and the Wii. Their Sonic games on both Wii/DS and PS3/360 did well. And the titles that kept them afloat ranged from Super Monkey Ball DS to Football Manager for the 360/PC. There is no defining "staying with Nintendo" sales pattern for them.
Nintendo's management wasn't a catch all saving grace for these companies. Yes, Nintendo's management helped Retro out in the early days. But that doesn't mean you can apply that example to every studio. Nintendo has plenty of studio management problems of its own and they aren't afraid to pull out of project, even if it dooms the developers (see this thread). At best, staying with Nintendo would have resulted in them working on random Nintendo IPs for the rest of their studio careers or, would have just resulted in the same situation we see here as any potential Wii titles would have fallen through, sold poorly and watched as Nintendo bailed out of their publishing deals.