You can probably go either way; if you leave them on, be sure that your 50V power connection (GRY-YEL) is connected to the end terminal with the stripped side of the diode or you will break things.
Your game already has an FL-11753 without diodes that's powering the diverter and uses identical circuity on the Fliptronics board. Fore reference, PN FL-11753-1 is the same coil without diodes. This is a fairly low power coil, similar in strength to the coil in a popup target, but you still wouldn't want to drive that for a long period of time which is why Williams is powering this from Flipper 4 on the Fliptronics board.
Fill disclosure: I do not own, nor have I ever worked on a Williams IJ.