Mustafa, my apologies for the delayed response! I've been thinking about your dilemma and this is what I've come up with. I'd make the most of the vertical space in the room so that you allow yourself maximum square footage for counter work space. If you're able to, I would suggest putting the refrigerator on the opposite wall (where the tall storage unit is in the sketch). Something similar to this:

Houzz is primarily for residential buildings but here are some images that might give you an idea of maximising space and light You basically want to keep a level of space and light so white or a soothing pale blue can work if the work is stressful. Good lighting and good natural light. Perhaps your management box in the center as four squares and slightly raised so you can see out the windows but also allow your staff to benefit. A rest and relaxation area for some breaks and a kitchen and toilets.

Lostinwoods, Covering the holes should not be a problem with a small dab of painters putty. If you are lucky or have planned enough the frames may cover the area left behind by hanger or clock. IMO, you should use colored photos with white frames as the room seems a bit dark as described by you. You may need some focus lights for the frames. Have a look at some of these photos. Thanks, Nitin Cornerstone Designs, Bangalore.

Wonder, It will be better if the current space between the two rooms is converted to a bedroom. The existing smaller bedroom could be a dining area with kitchen. Thanks, Nitin Cornerstone Designs, Bangalore.