Heller vs DC doesn't agree with you.The Founding Father's intent was a very separate force from the federal military when they used the word militia. Additionally, the first half and the second half are not as linked as people think.
"A well regulated Militia, being necessary to the security of a free State," is just a prefatory clause. It gives a context for the operative clause. It is just flavor to help the reader understand why the operative clause is being made. The operative clause is "the right of the people to keep and bear Arms, shall not be infringed". This is the only part of the phrase that matters or has any legal weight when analyzing the sentence structure.