Is there a way to tell fetchmail to ommit CAPA on some servers ?
Yes, by looking into the FAQ:
R11. My server is hanging or emitting errors on CAPA.
Your POP3 server is broken. You can work around this with the
declaration auth password in your .fetchmailrc.
Though the problem you reported should really be fixed. The repoll was
introduced because some servers did not authenticate after they gave an
error on CAPA, but it should not be retried when repolling. Somebody should
look into it, I have no time right now...