I've just deleted Vivec, Seyda Neen and Balmora's area by myself but CS still shows ca. 100+ objects per cell (what's pretty odd, due to cell's object list don't show anything). I've decided to stop my work at this point because I'm not going to make buggy mod. Thanks in advance!
Additional question
Can I find somewhere in scripts a part related to player's start position at very beginning of the game?