Is there any proof that the alt right has been openly emboldened to support this game in light of them not removing JonTron's lines? Because, as Kliklik pointed out, the devs might have noticed the giant shitstorm that brewed right after Playtonic removed JT from their game, and decided to do nothing as a result. It's entirely possible that the devs came to the conclusion that doing nothing would give the alt right one less grievance with which to feed their fake "the alt right is oppressed" campaign.
Regardless, you really can't blame a small indie studio for not wanting to kick the hive that is racist gamer shitlords. No one should be forced to choose that level of harassment, especially over three voice lines.