To me, he told the men to bring M alive to him was so HE could kill her. That's what he wanted to do all along, kill her personally. That's why he went to where she was testifying.
AND, upon further thinking, Bond fails to stop the bad guy. At the end of the movie what did he accomplish? He could've stayed on his island and the results would be pretty much the same.
How and why did he keep his job after such a cock up? "Sure, Bond, it was your idea to take M off the grid, rather than a secure location, and she did die, though maybe if it hadn't happened in the middle of no where... You can continue to work here."
The only way it all makes sense is if Bond and Fiennes were working WITH Silva to get rid of M.