Changeing their biochemistry I don't see the issue with. Unless there is proof of dramatic shift in their personality and actions. I.E a normal every day citizen suddenly becomes a serial killer with no remorse or sympahty. Killing who ever and what ever they want when and how ever they want.
I found this post interesting.
It actually occurs to me that the arguments for against Synthesis can be used against curing the genophage. One argument against, Synthesis is that you impose changes on everyone's physical composition. When you cure the genophage, you are impossing a cure on every Krogan on the planet, whether they want it or not. Who knows, perhaps some Krogan don't want to be cured. Yet Shep gives it to them whether they like it or not.
Now the argument for the genophage is that "It is for your own good." That argument can equally apply to Synthesis.
I think a lot depends on how each of us see Synthesis. If you have the view that it turns everyone into cyborgs, then that is not that pleasant.
If you have the view, that the changes are broadly cosmetic, basically to fool the reapers, then it it is less of a concern. From what I saw, I had the impression that synthesis had a greater impact on synthetics, effectively turning them into mortals. While the effect on organics was more cosmetic.
To be honest, the synthesis in itself is not my greatest concern. I can create my own interpretation that is acceptable if I want to. My two main concerns are as follows:
1) My first objection is actually more to do with politics than anything else. The reapers still exist as independent thinking creatures. Although they may not be initially hostile, they are still the most dominant force in the galaxy. They will also regard themselves as top of the food chain. So although they may cease the cycle, they may still want to dominate the lesser races. On the other hand, it is possible the end of the cycle could break the Reapers's unity and they could also fight each other as they take opposing philosophical positions. But I can't see how that would stop conflict in the future.
2) My second objection is that I hate that sickly green glow and the green eyes caused by synthesis. If the cosmetic effect didn't repulse me so much, I might accept it more. This is of course a personal taste issue. If you like the green glow, then I can imagine synthesis being appealing.