I actually think Green is lovely for a boy, but not for a girl as I don't think it's 'pretty' IYSWIM and you wanted pretty.
Gwyneth Paltrows little girl is called Apple and its gorgeous. People laughed but Clementine and Cherry are real names aren't they? As far as green goes, Jade, Violet, Scarlett, Rose, Ebony, Ash, Rusty, Olive, Hazel, and Sienna are all colours, so why not Green? What's the difference??
There are so many unusual names out there now and lots of foreign names too, so I honestly can't see it being a problem. My children's names are all really unusual and it hasn't caused them any problems at all, in fact they love their names. At their school most of the names are fairly different too, although it is an independent school - but i'm not sure if that makes a difference.
People will accept him for what he is, children are far more accepting than adults anyway. If you're worried give him a 'normal' middle name that you really like and he/she can use that if its a real problem.
The reality is that although everyone is thinking of things people will say to take the mickey, they do that anyway to normal names, both Christian names and surnames.
The problem with asking for opinions on names is that it tends to be a hugely emotive subject and some people (especially on Mumsnet) love to slam others, so you'll get those who weren't brave enough to do that saying its a bad thing as well as those who just want to be horrible because that's what they do on Mumsnet. I grant that some will genuinely be concerned for your child, but with a more usual middle name, it can be easily changed anyway.
By the time your baby grows up unusual names will be even more the norm, just as foreign names will be more common.
Where did names come from in the first place anyway? Most of them come from something that means something like April for eg, or June. There would have been a first for those too. What I'm saying is, what is a name exactly? It's something that came from something else.
I'd go ahead with a 'normal' middle name or two that you love as well and let them choose eventually.