Often times on flights to/from Eretz Yisroel there are people who put together a Minyan at the back of the plane. I for one always pray at my seat as I feel it can easily come to a Chillul Hashem. Is that correct?
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Indeed, some say to pray in one's seat, for precisely the concern you mentioned, of Chillul Hashem.
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.
Who says that if one davened shemoneh esrei(on an airplane) in their seat they do not need to daven again and may even lchatchila sit if they will be bothered by standing . She'eris Yosef brings this as a proof for davening by ones seat.
See Halichos Shlomo pg 95 who holds one should daven shmoneh esrei sitting down and not in the aisles since it disturbs others and one should not do that.
Rav Ovadia Yosef was noheg himself to daven b'yechidus on airplanes because he did not want to disturb others (gezel sheina)
Rav Wosner held that if one can daven shomeneh esrei standing adjacent to their seat(not in aisles) that's the best but if it is not possible to do that due to the tight space and one would be bothering the person next to them they should daven sitting. Regardless of what one does if the seat belt light comes on one must go to their seat immediately and buckle up even during the amida and finish in their seat since it is a sakana( chamira sekanta m'issura).
See She'eiris Yosef(Rav Shlomo Wahrman) quoted by Rav Hershel Schachter,a good overview on the topic and where I got the above answers from.
Rav Avigdor Nevenzahl Shlit"a the former Chief Rabbi of the Old city and foremost student of Rav Shlomo Zalman Auerbach, told me that to daven in a minyan on the plane bothers people and it therefore it is better to daven in your seat.
I don't see it as hilul H', of course assuming you don't bother people and ask for the crew permission and checking which time is not good for them (like the times they serve meals there's a lot of movement to prepare etc, so they need the space)
of course if you just stand up on the middle of the way and bother people would be a hilul H', but this is a general rule and doesn't apply specifically to planes