Leeks seem too milky, runny, should they have thickened?

MLE Phillips - no, I don't think you should have omitted the water. I think it's there to help the leeks cook some before the cream becomes thickened, too-condensed or even burned.
For next time, I might cook or steam the leeks first, then drain and add them to the cream.
For this time, to thicken up the current batch, I would not add flour (it will be uncooked and give a funny taste).
Options. Either simmer the mixture on a low heat to help some of the water left in the mixture evaporate. Or, some cornstarch (about 1-2 tsp) mixed with cold water (about 2-4 tsp), then added to leek-cream mixture and heated. This is common ingredient/technique to thicken sauces without changing the taste.