The Talented Mr. Ripley (1999)

Answer: After running into Meredith, Tom's plan was to stay in the cabin with Peter the entire trip to avoid them seeing one another. But after Tom makes that suggestion, Peter tells Tom that he seen him kissing Meredith. He couldn't avoid or kill her since Peter already saw her. Family members also saw Tom with Meredith. If Meredith suddenly vanished or was killed I'm quite sure there'd be an investigation. Peter was the only option. No one is on board to report Peter missing. Once the boat docks, Tom will be long gone before they discover Peters body. Unlike Meredith, her family would be looking for her immediately since they're traveling together. I'm quite sure he'd much rather have killed Meredith, she meant nothing to him.

Answer: Meredith was travelling with many other people and he can't kill all of them, so he has to kill Peter. Anthony Minghella discusses this in the audio commentary of the film.

Answer: I saw a lot of reviews saying killing Meredith would be harder because she traveled with a lot of people on the ship. Considering that Tom was able to figure out the old trick where he made Meredith to coincidentally meet up with Peter and Marge in a cafe, I'm pretty sure he could up with the same plot to tell Meredith to meet him somewhere around the corner of the ship too, say in the middle of the night to look at the moon etc. Peter beforehand can be exhausted due to consumption of alcohol or had steamy session of coitus so he could never find out that Peter went out to see Meredith. I don't know how the cruise ship of the 50s worked out at the time but there must be a range of dinner time where people go to a hall for their meals - therefore Tom could persuade Meredith to have some alone time at her cabin while the rest of her Cos were having dinner. Since Meredith was infatuated of him, anything what Tom could have said or planed something with her she would have agreed.