Yeah, there's definitely some timing to it... You basically want to hit the jump button the moment before hitting the water, but not too early that it counts as a double-jump and you lose out on some momentum. Still, better to err a little on the early side than on the late side. Properly timed, water skimming is a very speedy mode of travel.
No idea about the welcoming committee though, haven't been over there yet myself. Could potentially try sneaking? Although there are occasions where someone locked onto you will stay locked even through stealth...
On that note, for anyone who hasn't used a midnight robe yet, give it a go for funsies. It doesn't actually seem to care about time of day, it's reusable, and it goes on top of your armor/equipment instead of supplanting it. And the detection decrease is massive; your detection circles are reduced to like half of their normal size.
EDIT: Okay yeah, just took a quick trip over there, and I'm pretty sure that's supposed to happen. The dudes will target you regardless of stealth and do that funky move of theirs to delete you so the story can progress. If you're quick, you can actually run up to them while they're on the ground and initiate a proper battle with them, where they're not nearly as dangerous... Still very much playing by their own rules, but eminently beatable. I ended up killing like 7 of them with my loadout before going down, despite there only being about 5 of them on the island... They come back shortly after being defeated (even after massive overkill) to add their hurled owies to the crowd until you're eventually overwhelmed.