DaMoshe:
While I sympathize with your feelings in that story, I think that they made the correct decision with no ill-will intended, no lack of Ahavas Yisrael, and you also should not take offense for this same reason, as follows.
It is not at all uncommon for people who wear a knitted kipah to use a different havara than the traditional observant havara, such as substituting a patach for a kamatz and a taf in place of a saf (or thaf). (We’ll ignore the reason they do so, for this purpose.)
While this havara may fit a sefardi shul, as that is their mesorah, it does not make sense for an Ashkenazi shul whose mesorah is, for example, to distinguish between kamatz and patach and taf and saf.
So it makes sense that they would not offer the amud to someone wearing a knitted kippah and that this has nothing to do with their presumably fine level of Ahavas Yisrael.
Ahavas Yisrael is a wonderful thing, and hearing a nice chazan is also nice, but neither should cause mesorah to go “out the window”.