I don't know if it is within Eywa's influence to heal serious birth defects that have their cause on the genetic level, especially after the birth of that organism. Once a genetic sequence has been established, I would expect it cannot be altered anymore, not even by Eywa.
I do think it makes a lot of sense for the Na'vi to accept an individual with a birth defect, and see them as special and that they wouldn't always want to fix everything in the same way humans do. At the same time, there appears to be a culture in the Omaticaya and Metkayina clans that implies that being useless is not seen as a good thing in their society. The Omaticaya wanted to cure Jake of his 'insanity' and turn him into a productive individual and the Metkayina didn't want the Sully family to suffer the shame of being useless, so they wanted them to be productive as well.
So I am thinking a Na'vi with dwarfism could face a variety of difficulties and it might in the end depend on the Olo'eyktan's and Tsahik's personal views on how such an individual could fit within the clan (or not fit at all).
I was thinking of that darker undercurrent, and it's definitely a possibility - though if we look at pre-industrial civilizations on Earth (either non agrarian or early agrarian) it seems that the attitudes towards disabilities, birth defects and old age infirmity seems to correlate very strongly with the degree of resource availability and physical security of the society.
Societies that had very low resource stress and a good degree of security seem generally to have taken a more positive, or at least tolerent view, of "useless" people and often found roles for them - "useless", of course being somewhat subjective, given that spiritual (perhaps "shamanic") roles held a non-tangible but extremely valued role in pretty much every pre-industrial society, and arguably still do today (you'll find few towns in the west where we don't have a paid priest of some description) In Ancient Egypt dwarfism was recognised and held a secure and accepted social niche, and we know some other birth defects did not preclude social inclusion. By contrast, the inuit - possibly one of the most resource stressed cultures we know of - had no choice prior to the 20th century, except to take their elderly and infirm out onto ice floes and abandon them to their fate during in times of famine - something that was frequent enough in their extremely harsh climate that this had become a recognised and accepted, if unhappy, practice.
I would argue that the Na'vi clans we have seen so far lead relatively unstressed existences - their climate is benign, and resources abundant for their limited numbers, putting little pressure on them to rid themselves (one way or another) of "useless" people (the Metkayina wanted to teach the unskilled newcomers after all - not just shun them - and these were "outsiders", not true members of the clan).
It could easily be imagined, though, that if human colonisation of Pandora were to continue, that the driving of the Na'vi from their home lands and the over-exploitation of resources by the humans will stress Na'vi culture to breaking point, and that it would become *much* more violent, stratified and intolerant of any kind of diversity - much as New World societies (especially in central America and Mexico) did during the early years of Spanish conquest and settlement.