How should I remove the water from my pool cover?
The water in the pool will also be gross, so I wouldn't rule out option 1.  Especially if you'd otherwise be refilling the pool with a water source that has metals or other problematic contaminants.

Option 2 will work if and only if you can get the siphon hose outlet to a lower point than the water on the cover.  If you can reach that level then I would suck it up (pun intended) and use this option.

There are automatic pool cover pumps designed specifically to run when there's water on the cover and then shut off.  Cheap ones are under $50, so not a bad option either.

You've covered all the options.  I've done all three, and now have a mesh cover that lets water drain into the pool when it's on.