One of the unspoken rules that all alchemists are expected to adhere to is "Be Thou For The People" - in other words, alchemy is intended to be used for the good of mankind. Most consider this to imply that a pacifistic stance should be taken, or at least a stance of general nonaggression - that alchemy should be used primarily for creation or healing purposes. However, there are some that believe that defending one's country is a fair interpretation of that unspoken rule, that using our skills to serve the military is, indeed, acting for the good of our people. Both are valid interpretations; given that I served the military myself, it should probably be obvious what my beliefs lean toward. But the general population doesn't agree with those of us who served, and continue to serve, our military, believing in the more pacifistic stance; they insist that we have no morals, considering us to have sold ourselves to the government for money or military prestige. Admittedly, our standards for what we will and will not do have to be lowered quite a bit once we become State Alchemists; we're expected to give the military our complete obedience while we're under their employ.
However, arguably lowered standards or not, there are some things that are considered an abomination unto both humanity and nature in general; there were individuals in that war that were using alchemy in ways that even State Alchemists would find abhorrent. I didn't agree with the way they wanted to utilize what they had created; this...conflict of interests, I suppose you could call it, quickly turned violent.
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However, arguably lowered standards or not, there are some things that are considered an abomination unto both humanity and nature in general; there were individuals in that war that were using alchemy in ways that even State Alchemists would find abhorrent. I didn't agree with the way they wanted to utilize what they had created; this...conflict of interests, I suppose you could call it, quickly turned violent.