The problem is the system inherited from British rule (before Israel's independence at midnight tonight in 1948 ), which set up religious courts to govern each community. This left no secular option, nor an option for inter-religious marriages. Since the religious courts (regardless of religion) are quite orthodox, they're not about to start performing gay marriages.
The good news is that Israel does recognize such marriages performed abroad.
Furthermore Israeli courts have recognized gay couples under common law marriage laws.
Still work left to be done, but starting from a pretty good foundation of past accomplishments.