Enzymatic Reclaimer should only accept butchered meat.

[Sundance]

The ideas you propose would certainly make things more interesting, but where are these hungry wraiths and changelings? As far as I know they seem to get along just fine under the current system. They don't need any more easy targets to farm points with. If this was implemented the points received from claiming a reclaimed corpse should be lessened.

A closer look at balancing:
You could halve the dna points for changeling. That way a reclaimed corpse would be
- only worth 5 DNA points (negative)
- Not get any benefit of adding souls to the hivemind.(negative)
- But still counts towards objective (positive)
For wraith, 
- halve the WP regen gain (negative)
- still costs 20 WP (negative)
- halves the cooldown increase upon use (positive) 

And to address your point, I think it's wrong to view this as simply a farm for lings/wraiths. Yes there's an element of that but remember.. this is in the crew's control. If everything is consumed then the crew kind of fucked up. 
Less aimed at wraiths, who are for the most part in a good position anyway, and more for lings.. who are a bit 50:50 when it comes to being good. Having a small leg up that doesn't actually directly harm anyone is a good thing!!

being able to reclaim a corpse is one of the few ways to prevent a wraith from feeding on it. i'm also not entirely sure but i think if you're cloning and reclaiming at an even ratio you'll generally end up net-positive on biomatter

Being in the morgue or generally out of sight is also a massive barrier against wraiths too. 
Perhaps a chaplain annointing a reclaimed corpse by smacking it with a bible even further reduces the WP gain to a 1/4? (And a normal one to 1/2?)

And yeah it probably shouldn't be a net positive. 90-95% net negative imo.