I absolutely love the blinking flags, it's one of the best things to happen in FH2. Before this regular conquest maps were just about racing from flag to another as there was one squad back-capping everything, this was already a douche thing to do in vanilla BF2 (so many Karkands and Jalalabads won just by being an asshole). It also brings pacing into push maps, as when you lose a flag, you organise defence on the next flag, instead of losing it immediately because someone has spent 15 minutes of a 20 minute match "precapping" a flag.
FH2 is about two big frontlines that smash against each other, not about hunting lone wolves sneaking behind your lines.
And besides, 90% of players don't even look at the map, so at most a back-capper has to deal with one or two enemies. Shouldn't be too much of a trouble to deal with that. This is a feature that's also been included in all modern BF games (since BF3 if I remember correctly), and it works well there too. And just like in FH2, most people don't even pay attention to it.