Mr. Morgenstern was correct in trying to rid the world of these creatures to ensure the mundane and nephilim population would be safe in the future and present times.
These creatures break the covenant laws every single day. The laws are set to keep us safe though they are just words with little to reinforce them. Spending time in the Silent City cells is not enough. These species can not exist and continue to cause the destruction of a bloodline with few carriers as it is.
The shadowhunters and the downworlders have both signed the accords, agreeing to peace between the two. So not only would that be breaking the accords Valentine's plan was to attack them at the accords signing when they were weapon less and defenseless.
And many times to this day have the accords been broken. They are merely words set upon paper to which have been signed and disregarded. The world is to dangerous a place as it is we need not add downworlders and demons to the mixture.
I bring up the case of Miss. Clarissa Morgenstern/Fairchild. Her mother Jocelyn Fairchild kept her daughter from this world in fear she would be harmed. Little success came however when she was brought into contact with a iodelon demon at club pandemonium. This bringing harm to her, her family, the New York institute residents and her friends.
The accords may have been broken many times but they were all just small fights. However planning to get rid of all of them at a peace signing! That's much more then simply breaking the accords. That's first, not right. Second, basically starting a war. How is starting a war going to keep mankind safe?
There are some downworlders that pose a threat to the law and to humans. So punish those ones. There are so many more that follow the law and accords and no reason to kill them.
I'm not suggesting that you must start a war to have peace yet many times throughout history it has worked. I am not a person that is all for a war but in times of crisis action must be takern. The nephilim are getting slaughtered daily and throughout the night by these creatures. Putting a pen to a paper is to often not enough. And who's to say that these downworlders will not at sometime turn against them. They already have knives at eachother's throats as it is.
These people could lead normal, pleasing lives if it weren't for such a threat. Jessamine Lovelace; "I wish to have a normal life. One in which I will not be kept up by my Mother of Father choking down holy water". It is not right that these beings are being forced into leading these lives. If they try to hide the rune removal is torture upon their bodies and sometimes death. Yet their blood may still reveal them.
It may me true that many times in history wars have brang peace however think of the many times they have not. Let's say nephilim lost the war. Then who would protect the humans? No one. Humans would be constantly dying at the hands of demons. That would definitely be peaceful.
A valid point though however there and multitudes of shadowhunters in hiding. They are disguised as our everyday Mundanes, they would be who shall be called to war if the Nephilim were to lose. And you of course always have the Iron Sisters within the Adamant Citadel and The Silent Brothers of The Silent Cities to aid if need be. They would be under the protection of their domains and are known to be the best fighters and hardest to kill. They would not fight the war unless there was dire need and even still they would almost defintely survive.
What if they didn't believe there was any dire need. Then your left with the shadowhunters who are outnumbered as it is. Add the greater demons plus there wouldn't be much surprise if any shadowhunters turned against themselves.