In regards to having eggs/larvae in the Flow Frames, you can freeze your Flow Frames to kill them, and then put them back in the super for the bees to clean up.
I would encourage you to read the thread here about how long it can take for the Flow Frames to be utilized, and different techniques to encourage the bees to use the Flow Frames without removing the queen excluder:
Inspecting the Flow Frames doesn’t take too long… the main point about the Flow Frames is the ease of harvesting, and no processing required.
The windows can be used to gauge how your super is going, but especially when your hive is new, and you are getting used to the Flow Frames/Flow Hive, we encourage people to inspect the Flow Frames so they can check their honey is capped, and therefore ripe.
If you are worried about foreign particles, just run the honey through a filter as others have mentioned on the forum, e.g. @Dawn_SD using (unused) stockings over her container.
If you are worried about raw honey - then heat your honey.
The Flow Frames have been designed so that if there is a bee in the cell, they shouldn’t get anything caught, e.g. legs or wings, because of the little gaps between the cells. But if you just check your Flow Frames are capped, then you won’t have any bees in your cells.