Guessing this is before the trade deadline. You want him to remain active or are you OK with him being in limbo through the process? If it is the latter, remove him from the 40 and, if he clears, add him back. Waivers is only really meant to do the two things you don't want to do.
Complete text from the GM Basics: "Attempt to have the player clear waivers for future decisions (demotion or trade). In order to demote a player out of options, he must clear waivers. In order to remove a player from the 40-man roster, he must clear waivers. In order to trade a player after the trade deadline, he must clear waivers. Prior to the trade deadline, a player that is claimed cannot be pulled back. After the trade deadline, he may be pulled back."