SomeIndeed, some say to pray in one's seat, for precisely the concern you mentioned, of Chillul Hashem.
Citations:According to this VosIzNeias article, an unnamed Manchester rabbi "told a meeting that it is better to pray in your seat rather than risk a disruption by standing in the aisle", and his motivation was concerned "about the impression made on potential passengers, especially if Jews simply got up and tried to pray in a minyan". Commenters on that article cite other rabbinic figures saying similarly.
According to another VosIzNeias article Rabbi Yehuda Leib Steinman also ruled that it is preferable to say Shemoneh Esrei on a plane sitting down.
This is all rather one-sided, in that I've presented rabbis who agree with your reasoning and conclusion. That is not to say that there might (in theory) be other rabbis who would disagree.