Sorry, but I agree that if there's a 'standard' shortening of a name, you have to accept that is what a lot of people will call your DC.
My MIL has fought the "his name is Jonathan" fight against her DS called by everyone as "Jon" since school. I was introduced to him as Jon. I have to remember around MIL to say Jonathan. It is only her and FIL who call him that now.
I have a friend with a DD called Elizabeth. She actually didn't tell anyone her DD was Elizabeth until she was about 5 months old, she introduced her as Beth. My friend said it was to avoid her being called Liz, and it's worked, but every other Elizabeth I know gets called Liz or Lizzie. The only ones who get Beth or Betty are introduced as that, and anyone introduced as Elizabeth gets called Liz.
Bit late now, but if thats the basic shortening, that's what his friends will call up to ask for when your DS is older and you'll look like my MIL slightly unhinged if you tell them there's noone by the name of Jake here but there's a Jacob (yes, MIL used to do that with anyone calling for Jon, with her other DS she has the good sense to use a 4 letter name with no shortenings).