I think the problem is that Messianic Judaism is simply not Judaism; it's another religion, essentially a peculiar form of Christianity.  They may claim to be Jews, but they are Christians by definition; namely, they believe in the divinity of Jesus and worship him accordingly (and they study the "New Testament", the Christian Bible).  In addition, Christianity is a proselytizing religion (regardless of whether or not individuals engage in proselytization is irrelevant), and the potential of proselytizing from "within", so to speak, is naturally seen as threatening by the gov't of Israel, for obvious reasons.

Your point about the Law of Return and its applicability is a good one.  I guess the question would then be whether what they are experiencing is
indeed 'antisemitism' and not some other, perhaps related, form of prejudice.  If Messianic Jews are targets of antisemitism like what occurred in Nazi Germany (in which they are targeted as Jews regardless of their conversion to Christianity) they probably should be allowed to immigrate, I would hope, under a special provision.  But are they actually targets of such acts now?  Regardless, discrimination against Messianics that are in Israel is deplorable, I agree there.