Personally, I'd like to see MangaDex head the direction of more accessibility rather than less, eventually offering a public API for apps and possibly even zip downloads for offline viewing. There isn't really a good reason to lock things down (aside from measures to prevent server abuse) when access to chapters and images are supposed to be public, and the primary distribution method of many prominent scanlators are zip downloads or unsecured online readers on their sites or even IRC. Only a very small minority (usually those obsessed with monetization) attempt to lock thing down, but those scanlators likely wouldn't upload to MangaDex first anyway.
Sadly, the most effective measure to take against dodgy aggregators is to encourage people not to visit and support them. Since most degrade image quality, have harmful ads, and/or watermark, it's always been mystery why some people even use such sites out of choice. This has been a problem for all the online readers hosting original untouched images which have existed over the years (MangaToshokan->Batoto->MangaDex), to the dismay of scanlators but no real solution. One thing in MangaDex's favor are upload rules 2.1.1 & 2.2 which are much less restrictive then Batoto's policy on such things, and should go a long way at avoiding dodgy aggregators becoming the only source of some types of content.