To be honest, I didn't really like the game nor this series too much. They merged several routes from the game together for the animation. Though I'm glad that they made a new ending for the animated series. From someone who has played the game which was already partially animated, it would've been like watching a recap if they kept it intact. And not to mention majority of the good endings were weak, full of plot holes and it wouldn't fit the alternate route they've created for this series.
An issue with this episode is that it probably was too much for people who didn't expect it, and it was probably in an unairable state by public standards, hence it wasn't aired on the UHF stations. Though if you've played the game or read up on SD, you should've been well aware of this possibility. And this possibility arose at around ep09 or 10 with Setsuna's incident. And it was justified in ep12 that Kotonoha believed this entire time that Sekai was behind Setsuna's affair with Makoto to prevent Kotonoha from getting close to him.
I think majority of the people are forgetting that this anime is a port from an eroge with a weak romance setting and infamous for the bloody scenes. Girls fall in love and stick with the main character for no reason. Nobody questions the fact that characters suddenly disappears out of the story line like they never existed, like all the side characters in SD in the end and their parents. Though they managed to fix some of this issue by merging several routes together.
With that said, I don't think they did a bad job with the ending with the source they were provided. It was something new indeed. You really can't compare ep12 to what happened in the game since the routes taken are completely different and pushed Kotonoha into a higher psychopathic state, which is shown by her actions taken. As I've stated earlier, I expected a bad ending from the beginning of this series, so it met my expectations by displaying the gruesome scenes.
I think the boat scene at the end was a mere coincidence as Kotonoha mentioned about going on a yacht trip with Makoto in the previous episodes as someone else has mentioned. As already having to heavily edit the piece for airing on at-x, I really doubt they would waste their valuable resources to satisfy the fans for a brief humor.
The "Nice boat." comment spread on the Japanese net like a wildfire and has its own definition (Source in Japanese):
http://d.hatena.ne.jp/keyword/Nice%20boat
Anyway, as I've said before, they did a decent job for what they were provided. Give the ending 9/10. But overall the series was about a 7/10. I think the series would've been worse if they just left the game intact with the plot holes.