The Blood Ravens are also quite at odds with the codex, their Librarians encouraging the Chapter to various acts outside the bounds of the Codex.
The Blood Ravens are dodgy to say the least. They keep forbidden knowledge in their libraries, they have a huge stash of alien weaponry on one of their battle-barges, plus they try to hide it if any of their marines suffer mutations. Even without the fact that their chapter master is a pawn of Nurgle, if the Inquisition had to have a look around their ships, I'm pretty sure they'd be declared excommunicate traitors very quickly. As such, not strictly following the codex astartes is the least of their problems.
In general though, I agree that the codex can be more of a hinderance than an asset at times. When the UM tried to apply the codex in the 1st Tyrannic War they pretty much got slaughtered (man, must their faces have been red). Also, other than the remnants of the original loyalist legions, there aren't that many chapters who still specialise in a specific areas of combat (the Blood Ravens & Soul Drinkers being some of the exceptions).
I don't think the fact that some of the chapters have organs that don't work properly anymore is the result of time. I mean, chapters such as the Utramarines, Dark Angels & White Scars still seem to have properly functioning geneseed and their geneseed is just as old as that of the Imperial Fist or Raven Guard. I think that's more to do with how the different chapters have handled, implanted and protected their geneseed rather than the passing of time.