Now that Blizzard has made it completely clear in the patch notes that they consider abusing a secure code path this way to be an exploit, you can be certain that any evidence they discover of people still using it will be dealt with harshly. There is no longer any "innocent" excuse for it.
Even in PvE, players may still find your macroed actions suspicious, and could report them for any number of reasons. Consider the following scenarios:
"I was in a dungeon with a rogue today whose interrupts seemed to be timed exceptionally well. He was even interrupting casts that posed no threat and rogues would normally ignore. According to the combat log, he didn't miss a single one. It seemed suspicious so I thought I'd report it."
"In our Ulduar raid tonight, I saw one of our holy paladins go from his typical 15% overhealing done all the way down to 2% overhealing done, with no extra casualties. Our raid leader is now not satisfied with the rest of us. I'm almost certain the pally must have been using a hack, so I'd appreciate it if you'd investigate what happened."
"I saw an unholy DK killing quest mobs for one of the Icecrown dailies today. I was really impressed with how consistent his rotation was. When I asked him how he managed to do it, he said it was a secret and if he told me, he'd have to kill me. I know he was joking about that last part, but his timing really did seem too-good-to-be-true. I'm not accusing him of cheating, but if there's an exploit out there, I'm sure Blizzard would want to know and look into it."
As you can see, it's certainly possible for well-intentioned players to notice your improved performance. If they observe it long enough, they're likely to become suspicious. If your actions affect them, or if they simply "want to do the right thing", they may even report you for it.
Whether or not Blizzard can directly detect abuse when players block the upgraded DevTools remains to be seen. Since this requires the removal, renaming, or modification of an entire archive file that's normally expected to be present at runtime, it's quite possible that it can be easily detected and communicated back to them. To me, it seems like there is excessive risk in this workaround and it's one I won't be trying with my main account. (Your tolerances for risk may be higher, in which case, I wish you good luck!)
In any case, you should not be storing any /dump macros on Blizzard's servers, as has previously been mentioned. Those servers themselves don't exactly know whether macros are being synchronized (it's purely a client setting), they only know the last time the macros were uploaded or downloaded. So (pardon the double negative) not synchronizing your macros may not be a red flag for them.
Another way for Blizzard to investigate this is to find patterns in their server combat processing logs. Since these macros tend to be extremely precise, this makes patterns even easier for Blizzard to find. Combine that with the fact that thousands of players are typically copying and pasting the exact same macros using the same sequences of abilities and timing, and Blizzard may even be able to automate this kind of suspicious activity detection.
Blizzard should have resigned all their signed addon code and included a new key in the WoW executable to match the new versions. Instead, they just hacked together a quick change to the devtools to prevent casual or even unintentional abuse of the secure code path. It's likely that a "real" fix will come along in 3.2.1 or 3.2.2 after the few good UI developers Blizzard still has can be ripped away from the Next-Gen-MMO project they've been reassigned to.
So, if you're brave, enjoy it while it lasts!