While I dislike dropping an entry which is in kokugos, in this case it's probably the best solution.

I agree. I think this entry is more trouble than it's worth.

Isn't the best option to just delete this entry?

異なり	10424366	  
異なります	8891031

The problem here is that when someone encounters 異なり in the wild it's almost invariably the masu stem of 異なる, so this entry for 異なり is potentially misleading, Fortunately, the meaning is fairly close to that of 異なる. I think we need to keep the ことなり there, but [sk] is probably an appropriate tagging.
One issue is how text-glossing systems would handle 異なり. In WWWJDIC I use a special glossing file which combines this entry with the masu stem of the verb:
 - 異なり 【けなり; ことなり(ok)】 (adj-f) unlike; unique; unusual; 《verb stem》 異なる : 異なる(P); 異る 【ことなる】 ; (v5r,vi) to differ; to be different; to disagree; to vary; to diverge
Maybe that's anough, but a separate 異なり/ことなり may be appropriate too.

@@ -8,0 +9,4 @@
+</r_ele>
+<r_ele>
+<reb>ことなり</reb>
+<re_inf>&sk;</re_inf>

https://jisho.org/forum/64aa24a012a53716a8000000-dictionary-says-kotonariis-an-outdated-form

As it is now, this entry is causing confusion with the masu-stem of 異なる. See the referenced forum post.

If nikk is the only reference with ことなり, I think we can drop the reading. The "異なり【ことなり】" part of the term "異なり語数" doesn't seem to be related to this entry.

Since -なり adjectives are archaic, I think it might be okay to add a [arch] tag here. This will help inform readers that this entry doesn't refer to the masu-stem of 異なる.

@@ -10,4 +9,0 @@
-<r_ele>
-<reb>ことなり</reb>
-<re_inf>&ok;</re_inf>
-</r_ele>
@@ -15,0 +12 @@
+<misc>&arch;</misc>