Several JEs' glosses of "deify":
神として祭る	851
神格化する	4991 <- we have 神格化/deification
神とする	8044
神に祭る	81

Perhaps we could have an entry for 神とする. 
I'm no longer trying to use JMdict as a reverse search source, although it can be useful at times.

The reason for at least one xref is not explanatory, it is this is not the best term for "deify". 神格化 seams to be objectively preferable in terms of nuance and n-gram counts.

If you search jmdict for "deify" today, this is the only term that comes up. This is misleading as an E->J entry.  

There are a number of xrefs of in jmdict of the form:
[rare term] -> [probably what you actually want]

For deify, "神と崇める" isn't rare, but "神格化" is "probably what you actually want" if you got here by searching "deify".

I'm not sure if there is any practical remedy to this when all of the "deify" terms are under "deification".  It's certainly not a problem limited to this entry though, I don't know if there is a practical solution.

神と崇める	4362
神とあがめる	1083
GG5: 神と崇める treat sb as a god; deify sb.
中辞典 too.

I'd keep it, I think the と usage needs to be shown.
I don't think those xrefs help.

@@ -5,0 +6,3 @@
+</k_ele>
+<k_ele>
+<keb>神とあがめる</keb>
@@ -13,3 +15,0 @@
-<xref type="see" seq="1765230">神格化・しんかくか</xref>
-<xref type="see" seq="1295250">祭る・まつる・1</xref>
-<xref type="see" seq="2180460">神聖視・しんせいし</xref>

I don't think this should be an entry. We would reject any と/として[verb] construction if it were submitted today.

Reverso matches for "deify"
https://context.reverso.net/translation/english-japanese/deify
神格化して
神を祀る 13042
神格化を図った
自身を神聖視する　　（神聖視	18047)
天皇を東京で祭りたい
天皇に神格を与え
神として祀り
神格化されて

long-story-short, 神と崇める never appears
By searching the Japanese I got one match:
神と崇められた天皇 "revered as a deity"

https://ejje.weblio.jp/content/神とあがめられる
神とあがめられるの英語 (uses passive form)
be worshipped as a god

神と崇める	4362
神として崇める	1316

vs.

神格化	62535
神格化され	19701	  
神格化し	18322

I guess one can revere without worshipping, but "worship as a god" is more common in English.

I was going to discuss deletion, and suggest the removal of "to deify" as a gloss, because I think the xref terms are better.

Instead, I am going to advocate for keeping all of the higher-n-gram xrefs to "cheat".  The xrefs are often [vs] forms, and are listed under "deification", making them pretty much undiscoverable. (search for "deify", you'll never find them).

By adding these xrefs from a simple, understandable, common-enough-but less-common form, we expose all of the other "deify" entries to anyone doing such a search.

@@ -12,0 +13,5 @@
+<xref type="see" seq="1765230">神格化・しんかくか</xref>
+<xref type="see" seq="1295250">祭る・まつる・1</xref>
+<xref type="see" seq="2180460">神聖視・しんせいし</xref>
+<gloss>to revere as a god</gloss>
+<gloss>to worship as a god</gloss>