The points are yours to distribute. Since you want to stick to stealth and unarmed for this playthrough, go ahead and add points to those factors. There is no right and wrong.
However, do be sure that you put some points into other important areas as well. The importance of each skill, of course, depends on your play style. Keep in mind that you will need certain skills to complete some quests. Personally, I find Speech, medicine, barter and repair pretty useful.
If you want to be a good sniper you're going to have to add points into guns.
There is a 30 level cap (50 with all the DLCs installed), and you get a perk every two levels, so choose them carefully.
A character cannot be good at everything, so go forth and max out on what you want. You can always come back and play again to try different combinations.
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