No. The intent of the draft was to protect those who objected to bearing arms for religious/moral reasons from being forced by the government to bear arms against their will (essentially making any draft that didn't have consciencious objector allowance from being Constitutional). The line was removed at drafting because it was redundant: The First Amendment protects the free exercise of religion and barrs the government from declaring religious tennents illegal without a very compelling government interest... the government making war was not compelling enough of an interest to force religious pacifists to take up arms for the government... better that the U.S. should suffer military defeat than violate the beliefs in individual liberty.
It does not imply that the 2nd amendment was intended for military purposes, but rather for self-defense purposes (at the time, militia meant the able bodied men of a community who could muster to defend from attackers. While we think of the "Wild West" in terms of the Modern West of the U.S., in 1789 when the Bill of Rights was being drafted, the "Wild West" were the western most parts of the states that we today think of as the "East Coast" the French and Spain/Mexico and the British controlled much of what is West of the Appalachian Mountains today. The "wild west" was closer to home than we tend to think of it and people did live far enough into the wilderness that the "community" that could form the militia might just be the patriarch of the homestead. It was so important that not only did the founders think to make sure that the right to weapons was essential, not only did they draft this having just exited a sucessful war where their troops were just that and an armed rebellion that was even fresher in their mind, the match that ignited the powder keg of the Revolutionary war was the British attempting to sieze weapons from Lexington and Concord that the people in those towns needed for survival. The "Shot Heard 'Round the World" was shot over the right of the colonists to keep and bear arms and the founders were well aware of what they were fighting for.
To further validate the individual right to the people, President Thomas Jefferson, who had a hand in writing the Bill of Rights, when asked about if this allowed a merchant to place cannons on his ship, responded with essentially "That's the reason I wrote the Amendment in the First Place."