The ponies don't want humans, and if Lyra's gonna keep acting like one (even if it's against her will), she's gonna get chased out, in There She Is, there's a city of cats, and a city of rabbits, Doki (the rabbit) happened to meet up with Nabi (the cat) at vending machines, Doki instantly fell in love with Nabi, but Nabi felt the opposite, eventually, the two cities heard of this relationship and wanted to put an end to it
Kind of a stretch but it's mostly of Lyra running from everyone else who are carrying signs and such reminded me of There She Is