For the short term, first 6 months you could easily put the nursery in your room in the separate area. Long term not a great solution since after that kids will be likely going thru sleep training, harder to get down at night and may wake you both up more than you'd like.
Another couple options to consider, either now or long term. Is the guest room big enough that you could have his desk on one side and the guest bed on the other? Not sure how big his desk is but if it's just a size issue does he need/utilize all the space he has currently on it. If not maybe a smaller desk since most folks just have a flat screen monitor, laptop and printer he shouldn't need a monster desk. Maybe put file storage in a closet in the guest room to get it out of the way. Also long term have you thought of finishing out the basement and moving his office downstairs?
Re: Need a nursery and an office space.... Help me utilize space better.