Indeed, some say to pray in one's seat, for precisely the concern you mentioned, of Chillul Hashem.

According to this [VosIzNeias article][1], 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][2] 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. 

  [1]: http://www.vosizneias.com/43425/2009/11/19/manchester-uk-rabbi-dont-pray-with-minyan-on-a-plane/
  [2]: http://www.vosizneias.com/61173/2010/07/30/israel-rabbi-on-planes-shemoneh-esra-prayer-can-be-said-sitting-down/