‘Aleinu: U’moshav Ye’Karo or Kisei Khe’vo’do?

Someone asked on my previous post on ‘Aleinu:
1 - What is the meaning of U’moshav Ye’Karo, the seat of His homage is in the heavens?
2 - Why do some not say it?

This is the nusach in the Siddurim of R. Amram Gaon and R. Sa’adia Gaon. The Tur (Orach Chaim , Siman 133) mentions that some say, v’kisei khe’vo’do (Mahzor Roma), but that U’mosahv Ye’Karo should be said because the Sefer Hekhalos has the nusach, U’moshav Ye’Karo.

The combination of kisei and kavod is common in Tanach. Two examples:

Tehillm 9 has, ya’shav’ta le’khi’sei and has, yei’sheiv parallel to kis’o:

5: …Yashavta le’khisei shofet tzedek
For you have maintained my right and my cause; you sat in the throne judging right.

8: Va’Hashem le’olam yeshev konen la’mishpat kis’o
But the Lord shall endure for ever; he has prepared his throne for judgment.

Tehillm 103:
19: Hashem ba’sha’ma’yim hei’khin kis’o u’malkhuso ba’kol ma’sha’lah
The Lord has established his throne in the heavens; and his kingdom rules over all.

According to the Gra, the nusach should be: ve’kisei khe’vo’do, the throne of His glory.

In Mail-Jewish (http://www.ottmall.com/mj_ht_arch/v33/mj_v33i61.html#CSX) , Gilad J. Gevaryahu translated Professor Ismar Elobogen as saying:

The acceptance of this tefila was very controversial in Germany, where
there were repeated charges against the Jewish religion. These did not
subside for hundred of years and eventually led to the elimination of
the sentence 'shehem mishtachavim lahevel varik umitpalelim le'el lo
yoshia,' which still exists in manuscripts and Sephardic and other
siddurim. In about 1400 a Jewish mumar (an apostate) went to the
authorities and told them that in this sentence the Jews refers to
Jesus. His proof was that the gematria of varik equals 316 as does the
name Jesus. Liefmann-Milhausen, in his book _Nitzachon_ proved the
charges wrong [claiming inter alia that this tefila preceded
Christianity], nonetheless, the charges were repeated again and again.

The commentary, Barukh She-a’mar (p.199), by the author of the Torah Temimah, points out that ye’karo, has the same gematria as yeshu. Therefore, he concludes that the correct nusach should be, v’kisei khe’vo’do, which avoids this Christian leaning gematria.

Eliezer Segal says:

It did not take long for our nimble numerologists to run into an unexpected problem. The consonantal text of varik forms an anagram of the word yekaro, which means that the two words share the same gimatria. Yekaro means "his glory," as in the clause "and the throne of his glory is in the heavens above."
(University of Calgary: http://www.acs.ucalgary.ca/~elsegal/Shokel/000928_Aleinu.html)

In answer to the questions:
What is the meaning of U’moshav Ye’Karo, the seat of His homage is in the heavens? Why do some not say it?

The meaning is easily subjected to Christian interpretation and reference to yeshu by use of gematria. The other nusach, v’kisei khe’vo’do, is supported in earlier texts, as well, and has none of these issues.