I agree on the unfortunate "othering" of races in MLP. Zecora made me a little uncomfortable although she was a pretty cool character just in principle.
I thought this episode was well-done if you must do an inevitable "settlers vs. Indians tension" episode (it was certainly better than Avatar). But that doesn't make it not a problem. It's not a huge, irredeemable, damn-the-show-forever problem, but it's one that's worth acknowledging and talking about.
Like Lynxara says, that sort of writing is so easy to slip into your work without thinking, so I don't think it's right to just dismiss the criticism, even if the tone it's spoken in is kind of unfortunate.
(One thing I don't get, though, is what's with the snarking about the tipis? They're nomadic plains-dwellers, wasn't that kind of the standard domicile for tribes of the area during the time period in question?)