I think a problem comes in assuming that the "name above every name" is "Jesus".
Jesus/Yeshua was a common name at the time (http://www.jesus.org/is-jesus-god/names-of-jesus/jesus-an-ordinary-name.html). Joshua appears to been as common a Jewish name as John is in English. Even today the name Jesus is common in some parts of the world. However, the name/title which sets Jesus apart from everyone else is "Lord".
Luke 20:42 makes it clear that Psalm 110 is talking about Jesus, who as LORD, will have his enemies made a footstool, and will rule from Zion.
42 “For David himself says in the book of Psalms,
‘THE LORD SAID TO MY LORD,
“SIT AT MY RIGHT HAND
Jesus was given the ὄνομα (name) above every ὄνομα, and ὄνομα has variously been translated as name, character, fame, reputation.
It would be most natural to see that name or designation as "Lord", rather than "Jesus."
Regarding using "Jesus" instead of "Yeshua", we do that because the Greek manuscripts refer to him as Jesus, and the Greek texts are usually held by the Christian Church to be divinely inspired.
This is not some kind of conspiracy - because the New Testament writers most often quote from the LXX, all the distinctive names of God from the Hebrew scriptures are replaced by the terms 'God' and Lord'. The Apostles, whom the Church holds as inspired, didn't seem to have a problem with this.