Use ProtocolLib to make items glow without enchantments.

PLGlowWithEnchanting.java

import org.bukkit.Material;
import org.bukkit.command.Command;
import org.bukkit.command.CommandSender;
import org.bukkit.enchantments.Enchantment;
import org.bukkit.entity.Player;
import org.bukkit.inventory.ItemStack;
import org.bukkit.plugin.java.JavaPlugin;

import com.comphenix.protocol.Packets;
import com.comphenix.protocol.ProtocolLibrary;
import com.comphenix.protocol.events.ConnectionSide;
import com.comphenix.protocol.events.ListenerPriority;
import com.comphenix.protocol.events.PacketAdapter;
import com.comphenix.protocol.events.PacketEvent;
import com.comphenix.protocol.utility.MinecraftReflection;
import com.comphenix.protocol.wrappers.nbt.NbtCompound;
import com.comphenix.protocol.wrappers.nbt.NbtFactory;

public class ExampleMod extends JavaPlugin {
    @Override
	public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
		if (sender instanceof Player) {
			Player player = (Player) sender;
			
			// Get a CraftItemStack
			ItemStack stack = new ItemStack(Material.IRON_AXE, 1);
			stack = MinecraftReflection.getBukkitItemStack(stack);
			
			// We'll co-op Silk Touch 32 (as it doesn't make much sense) to mark this item as glowing
			stack.addUnsafeEnchantment(Enchantment.SILK_TOUCH, 32);
			player.getInventory().addItem(stack);
		}
		
		return true;
	}

	@Override
	public void onEnable() {
		ProtocolLibrary.getProtocolManager().addPacketListener(new PacketAdapter(
				this, ConnectionSide.SERVER_SIDE, ListenerPriority.HIGH, 
				Packets.Server.SET_SLOT, Packets.Server.WINDOW_ITEMS) {
			@Override
			public void onPacketSending(PacketEvent event) {
				if (event.getPacketID() == Packets.Server.SET_SLOT) {
					addGlow(new ItemStack[] { event.getPacket().getItemModifier().read(0) });
				} else {
					addGlow(event.getPacket().getItemArrayModifier().read(0));
				}
			}
		});
	}

	private void addGlow(ItemStack[] stacks) {
		for (ItemStack stack : stacks) {
			if (stack != null) {
				// Only update those stacks that have our flag enchantment
				if (stack.getEnchantmentLevel(Enchantment.SILK_TOUCH) == 32) {
					NbtCompound compound = (NbtCompound) NbtFactory.fromItemTag(stack);
					compound.put(NbtFactory.ofList("ench"));
				}
			}
		}
	}
}