Is the LaunchAgent from the vendor of the app, or is it something you created? If it's something you created, what command are you using to launch the application? Because the open command has a few flags that might be helpful. For example, according to the manpage for open, using the -j flag will cause it to hide the app as it opens it. There's also the -g flag which prevents it from coming to the foreground when opened.
Even if the agent comes from the vendor, you might be able to modify it to use one of those flags in whatever command it's using. I'm just not sure what the app is, or how the LaunchAgent is configured.
