The Law of Return does not recognise gay marriage and so therefore neither can the Law of Return. Legally this guys partner is no different from having a boyfriend and the non jewish partner of an unmarried couple. The Law of Return may not directly use the word marriage but that has always been assumed as its meaning. An unmarried man and woman cannot both make alliyah because one partner is not Jewish, they are not partners in any kind of legal way so its not recognised. Right now the Law of Return does not consider gay marriage legal marriage and so 1 of those men is eligible. Israel is certainly not a country that can be considered homophobic, the Tel Aviv tourist ministry has even been trying to promote Israel's gay bars etc abroad to try and attract gays to come visit. We have also given asylum in the past to gay palestinians who are being persecuted back home because of their sexuality. The IDF now allows soldiers to be openly gay. Israel is probably the only country in the region which tolerates homosexuality so I really don't think Israel can be accused of being intolerant towards homosexuals just because a gay couple has been refused citizenship under the law of return.
Clinton: U.S. must "make clear" to Putin that Russia cannot be creating chaos in Syria (Reuters)
from the article: Israel refuses citizenship for gay man married to Jewish immigrant