I don't have a copy of Campaign Operations, nor has anyone in my group, so I cannot comment as to these special rules using the Total Warfare boardgame rules.
In regards to Alpha Strike, my group has embraced SPAs, command abilities, and formations. These, particularly when combined with Forced Withdrawal rules, can create more enriching gameplay. For example, formations lose their special abilities when half of the formation is destroyed or crippled, meaning that gaining an advantage is no longer simply about destroying or crippling units. The same with Special Command Abilities, which are tied to designated commanders, making those units high value targets for reducing your opponent's abilities and options. So the possibility of losing these advantages also factors into the risk/reward choices a player makes during the game.
You may want to give some of the rules a test run outside of a campaign. There, you can gauge if the extra rules add to the gameplay, or stifle it with additional bookkeeping and reading.