kindlegen does support epub input. It may not like all legal ePubs, but it should produce a 100% compatible MOBI for Amazon (essentially by definition).
If the Sigil ePub does not convert cleanly to MOBI using mobigen, what I would try next is:
a) Convert from ePub to MOBI using Calibre, then
b) convert from MOBI to ePub using Calibre, then
c) convert from ePub to MOBI using kindlegen.
This is a very round about way to get a Kindle MOBI, but Amazon can hardly blame Calibre if kindlegen is what creates the MOBI.
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