I am not sure what the more experienced pony people would say, but here is my two pence for what it's worth: first if this pony is to be yours you can do whatever you like and make her how you would prefer her to be without worrying about resale value. Or indeed any other consideration.
Second, just tell everyone that you prefer her with blue hair / always wondered what she would look like with blue hair and THIS is why she has blue hair. Don't ever admit that the real reason is because you are not so good at the rehairing thing
. This is your custom after all, so your rules.
Good luck; it would be great to see how she turns out!