In my opinion it isn't the creation of morphs themselves the leads to weakness as much as it is poor husbandry. Keep in mind that the common analogy of dogs to herps doesn't mesh exactly. Dogs were drastically manipulated for specific tasks. The German Shepard for example was bred to have a low back end so that it would be advantaged as an animal that attacks taller bipeds (people). This bending of the BASIC PHYSICAL FORM of the dog though desirable in the short run led to hip problems for the dogs. This is a bit of a "gray" area type statement but the problem here isn't as much about the specifics of the genes as it is a mechanical problem. I don't think breeding out color or pattern mutations in herps could ever have quite the same level of impact as some of the problems we've seen with dogs.
Back to the husbandry thing, an example I have experience with and can site is the snow corn. When these first became available they were a very weak strain. As a primer, snow corns were "created" by crossing an amel corn with an anetheristic (sp?) corn to produce neonates that were "double" het for these two traits. Statistically, line breeding these double hets back to each other produces only 1 in 16 neonates with the desired snow phenotype so very few were produced from the F2 cross. Because outcrossing these would result in the same low ratio of snow production, there was a disincentive to do so. Consequently, the strain was bred sibling to sibling for several generations until problems started to appear. Since that time the strain has by necessity been outbred so that hardy snow corns are now the rule not the exception. This proves that at least in this case the issue was not of an inherent weakness in the gene combination but a lack of attention to proper husbandry. This isn't to say that there aren't examples where desirable morph mutations are also also associated with some deleterious effect, just that I'm unaware of any. In all cases in which I have any knowledge, attention to breeding and outcrossing have rectified health and fecundity problems that might have initially been associated with a given morph.
I honestly think that the biggest issue we have going on now is this locality thing. I understand "locality" issues from the perspective of a field guy 100% but fail to see where it is analogous to captive breeding! Nature doesn't erect "complete" barriers to gene flow between adjacent sub-specifics much less between mere populations defined by arbitrary data. For this reason, I only see two reasons to erect them in captivity. The first is to keep a rare locality line rare thereby maintaining price. In contrast where rarity of the founding population isn't an issue not only is price not an issue but enough have been taken into captivity to form the basis of a solid founding captive population so no harm done. In cases where founding stock is rare however, say coastal plains milk or some of the rare alterna or pit projects a strict insistence on locality breeding can easily lead to numerous inbred lines. Most of Tyrell NC coastals locality stocks for instance stem from only two wc animals. Similarly, most "legal" NJ stock go back to a single pair. Both strains could use an infusion of new genes from other locals but this is discouraged. How propagating numerous inbred lines serves the long-term interest of this forms is beyond me but the "ethic" is well entrenched. The second reason I see to erect artificial barriers to gene flow in captive populations is personal preference. To do so for this reason is perfectly acceptable but it doesn't explain willingness to overlook the issue of inbreeding?
I think that in the end we need to keep in mind that most of us are working towards the domestication of these herps. To that end a purebred animal is simply one capable of passing a similar suite of characteristics onto the next generation. Among the characteristics passed from generation to generation, I would count good health. If a breeder is working towards this end I would say job well done regardless if he/she is working with hybrids, morphs or wild type locality animals.