What you describe is a pretty common occurrence and based on what I can tell its also fairly traditional. While there may be several options to distribute communion to the choir, there does not appear to be a prescribed manner. The GIRM merely states:
While the priest is receiving the Sacrament, the Communion chant is begun…The singing is continued for as long as the Sacrament is being administered to the faithful. If, however, there is to be a hymn after Communion, the Communion chant should be ended in a timely manner.
Other than respectfully discussing other options with your choir director and pastor, there’s really not much else to do since it doesn’t appear to be incorrect.
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