Konoha would win, remeber they have Anbu, and the Anbu are really ninja-like, they could take whole troops in guerrilla like tactics, most of the ninjas in Konoha can do that, they are trained to work in small groups of highly organized tactics, and hit-and-run strategies. If this goes to an all out war, face to face in a field Amestirs would win, not without difficulty, since the elemental Jutsu can make a lot of damage, but if this goes into a guerrila like warfare Konoha can extermiante Amestris army.
The Team 7 can really make damage, Sakura is not only strong, she was trained to avoid attacks by a Sannin, as she showed that prowess in the fight with Sasori, and can aslo heal the group, Kakashi haves an undefined number of Jutsu, remember his nickname, the copy Ninja, he used Sharingan to learn almost any jutsu used against him. Naruto (Current) can lay waste over regular armies, he can move faster than the enhanced Shinobi senses of a Jounin such as Yamato can see, and as he taps into the Kyubi Chackra he haves an unholy ammount of stamina and regeneration, and if he uses Sennin mode and the cloak of Crimson Chakra he is going to rampage over Amestris army. Sai can create summons to protect him, and he can transport people throught air, and he can carry ninjas with long range elemental jutsus to act as bombers.
Also the Konoha troops have Shikamaru and his father, that are superb strategists, also at least 4 people that can see at great distances and with x rays eyes(Byakugan), and several other clans with useful abilities, as the Aburame clan can poison the enemy using their bugs, that cant be shoot down easily, and can even seem normal bugs to the Amestrians. Also they have supernatural medic teams, and unholy speed. This means that maybe they cannot dodge a sniper bullet directly aimed to them, but they can react and take cover against bullets barrages, or blind shooting. Also if the combat reaches close combat, the Shinobi have advantage. They can also manipulate the terrain, thus they can create trenches out of nowhere, they can flood the terrain, or create forest out of nowhere(Yamato) giving the Konoha army an extra edge over the modern weapons, and a tactical advantage as they can decide in which terrain to fight.
The Alchemists can be beaten by squads of elite ninjas (Water aligned to fight Roy Mustang for Example), or in individual fights with superb ninjas, such as Might Guy, Kakashi, Neji, Tsunade, Asuma...etc...