She had clear instructions to proceed no further, then climbed through a broken window towards Secret Service members who had guns drawn.

She was partway through the window to the hallway that leads directly to the congressional chambers and was attempting to get past the Secret Service members.

You don't mess with the Secret Service -- they have a very uncompromising view on protecting elected officials and will absolutely draw lines in the sand and firmly enforce them.

Edit: Secret Service were present, but the officer who shot was not a member. He was, however, protecting the immediate vicinity to where congresspeople were sheltering in place.