I was looking into this myself, and Wikipedia brings up this quote by Ben Sharpsteen:
We thought the name [Rover] was too common, so we had to look for something else. ... We changed it to Pluto the Pup ... but I don't honestly remember why."
And cites: Brasch, Walter M. (1983). Cartoon Monikers: An Insight into the Animation Industry. Bowling Green, OH: Bowling Green University Popular Press. p. 69. ISBN 0-87972-244-4.
The article goes on to say:
Some Disney animators reportedly believed that Walt Disney chose the name to capitalize on the sensation of the newly named planet.
And cites: Boyle, Alan. The Case for Pluto: How a Little Planet Made a Big Difference. Hoboken, NJ: John Wiley & Sons, 2009. p. 49.
It's there any more information on the history of Pluto's name? Which animators suspected Walt Disney was capitalising on the planet? Was the planet a big enough deal at the time for that to make sense?
Was he even directly involved in the naming? Pluto appears in The Chain Gang (1930) which was produced by Disney but involved many more people. I don't know how much Disney got involved in naming etc at that stage of his career.