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So we know that for warp transit you need an active Gellar Field to prevent Daemons from materializing within a ship while in the warp.

These Daemons would presumably be more powerful than those that are encountered in the materium because they don't need to expend the effort they ussually would to possess a psyker or a summoning ritual or create a warprift.

Regardless, the Eye of Terror is described as an area where the materium and immaterium are merged.

Does it follow then, that when ships are traversing the area of space of the Eye of Terror without activating their warp drive (ie: at sub-FTL speeds), would those ships gain some manner of protection by activating their Gellar Field?

I would imagine that moving in "merged space" is pretty much the same as moving in the warp, the rules are bent and you'd be able to go at FTL speeds anyway. Time would be altered as well, to boot.