I could see i happening, if they ever expand Octo Valley or did more amiibo, and I wouldn't have a problem with it (especially Hero Splatling, I wanna wreck Octo Valley with it so much, it'd be even more fun than Kraken-racing through stages with the Squid amiibo), but I don't expect it any time soon.
Still, it could happen, and it could arguably make the game a bit better.
I think of Octo Valley as a training mode for online play, since you can learn and practice quite a few basic things through playing it (the Octoling levels in particular, since they act like Inklings for the most part). And the amiibo add to this, since they give you an environment in which to test out the Charger and Roller weapon-types (well, the generic versions, anyway) in a fairly stable environment (regular levels) and on enemies that act like an approximation of online players (the Octoling levels); the Squid amiibo is purely for fun though (though Kraken Kart is damn fun). Still, I find myself wondering why basic versions of every weapon type (Shooters/Chargers/Rollers are already repped, but Blaster and Inkbrush aren't, and I think Bucket Slosher and Splatling should be too if we're adding more Hero weapons) wouldn't be given Hero versions, if only for use after beating Octo Valley (or at least going far enough into it), so you could get the hang of those as well and practice splatting Octolings to get used to them. Also, Hero Brush would be interesting to see in Octo Valley, possibly for time-limit challenges (would be harder than the Kraken time-limit levels, that's for sure).
I'd rather it not be amiibo-exclusive, though I'd understand if it were, I just want to be able to use them in single player in some capacity. Though if they did go that route, I wonder who they would make the amiibos of.