What they're doing now is respectful but the situation in the first place isn't. Nintendo would never out source a mainline Mario, Zelda or Pokémon game to some Namco b-team. That's the sort of thing they do for franchises that aren't enough of a priority for them to assign their internal teams to. In general Nintendo seems to regard Metroid as that weird series that the American market appears to like but the Japanese one doesn't.
Hmmm I guess they're kind of right though? Metroid just isn't a sales cannon usually, and the dedicated fanbase it does have has a very narrow idea of what it wants and is swift to reject most attempts at diversification (Federation Force, Other M).
I don't know if I agree that outsourcing inherently signals disdain for a franchise though...
-Flagship/Capcom did 4 Zelda games, 3 of which were the respective, well, flagship Zelda titles for their respective platforms.
-Star Fox Zero & Guard were outsourced to PlatinumGames and Nintendo saw fit to send over Mr. Miyamoto himself to guide development.
-Same story with Metroid: Samus Returns; Sakamoto was the producer after being impressed by MercurySteam's earlier pitch for a Fusion remake.
-Amusement Vision/Sega did F-Zero so well Nintendo reportedly asked to see the source code.
-Lots of remakes (Ocarina of Time, Majora's Mask, Wind Waker, Twilight Princess, Luigi's Mansion, WarioWare Gold) have been outsourced so Nintendo can continue to develop new games internally, I doubt those games' respective reputations were just thrown under the bus to make a quick nostalgia buck, they're mostly polished remasters.
-Smash Bros. has been noted above already.
Basically, for a publisher with such narrow development bandwidth as Nintendo, they're bound to turn to outsourcing if they really want to produce 12 games a year. They've done so for remakes (Zelda), but also for franchise revivals (Metroid 2), and marquee titles (Pokkén Tournament, Smash, Warriors games).
As a Metroid fan, I absolutely understand the wish for Nintendo to treat the series as a third pillar behind Mario and Zelda. But the reality is that Mario Kart, Smash, Animal Crossing, Splatoon, Pokémon, Kirby, the recent solo Yoshi games, Donkey Kong, and arguably even Fire Emblem nowadays are all more popular franchises. Most of them sell better than Metroid too, Splatoon and Fire Emblem are still behind in unit sales but have seen significant popularity boosts recently - and Splatoon already sits at 12.4 million sold copies against Metroid's 17.4m, with just 2 games under its belt.
I guess I see the initial plan for Metroid Prime 4 not as disrespectfully handing it to "Namco's B-team", but rather Nintendo trying a new production model and it didn't pan out the way they liked. I'd highly doubt that Namco wouldn't put some talented developers on the project; Prime 4 would be their most high-profile work with Nintendo since the GameCube days (Star Fox Assault, Donkey Konga 1-3, Mario Baseball), I'd be surprised if they didn't jump at that opportunity.