I understand the objection. My impression too is that in the modern day, 'Sekte' does still sometimes seem to be used in German with a pejorative tone more like 'cult' in English, and even to refer to groups that are not in fact weird or unorthodox at all, merely non-EKD or non-Catholic. So a better word in English might sometimes really just be '(religious) denomination.' (Or possibly '(religious) movement,' but that sounds more temporary and less organized.)
However, in a historic context, small groups that opposed the majority in a religion and did not survive (say, the Essenes, or the Albigensians, or whoever) are indeed called sects in English and (I presume) Sekten in German, and so are modern groups that really are small and unorthodox (in fact, not just in the mind of the speaker). So there certainly are contexts in which it's right, even if in other contexts we should be cautious about automatically translating it 1:1.
Short answer: No, it shouldn't be deleted, since it's only a semi-false friend, not a totally false one.
My own view is that it may be misleading not to offer a couple of other translations D>E, but after some other discussions we've had here about religious terminology, I don't really want to open that can of worms.