I did a Holyland cruise with my parents last fall on Odyssey. It was fantastic and a dream come true for my Mom as she's always dreamed of visiting Israel. Yes, a cruise doesn't give much time for an in depth visit, but it worked for us at the time.
Some tips...
Spend the money and hire a private driver/guide. We had one for the 3 days in Israel and it was really nice to have flexibility and the ability to customize a bit. It also allowed us to take full advantage of his connections at the sites and often get what seemed like VIP treatment.
The ship overnighted in Ashod, so we had two days in the area. We spent the night in Jerusalem and while we arrived at the hotel at dinner time and were exhausted from a long day, it was well worth it. We were talking at dinner about how miserable a drive back to the ship would be at that moment. In the morning, our driver picked us up and we carried on. So definitely consider this option.
The whole cruise was amazing, but Israel was the highlight. Just be flexible with traffic, security issues and crowds.