Palps wanted the two together, and away from the jedi, hence his urging to send the two together to Naboo. He knew Anakin cared for her...and because of this, he had to hide this fact from the Jedi, which therefore made him separate further. And her death, which he more or less had planned from the start, would only drive Anakin insane with rage, into the Vader we all know...
so not only does he "allow" this, he supports it.