Still talking in those "highly unlikely" terms? In other words it's just conjecture, no fact.
Israel has it's own cruise missile, the Popeye, that could theoretically carry nukes. In fact, the US military has bought a few of them. What the advantage of the Harpoon is over the Popeye I don't know but it isn't as simple as being able to carry a nuke since Israel already had that capability. None of that matters, anyway - not all of our Harpoons carry nukes so they are obviously used for conventional warfare, too.
You might want to check some other sources on that news item, too. Most of them don't say "cruise missiles armed with nuclear warheads" they say "nuclear capable cruise missiles" - big difference! Obviously the article was slanted to stir the pot and promote fear, not report the facts.