Taking risks in a story is...er...risky, but it has been done successfully many times.
Jules Verne, HG Wells, George Orwell and a host of other writers have written what was in their heart and made a living out of their writing. Verne and Wells risked being made fools of by future science.
In his story about a journey to the moon, Verne had the astronauts put inside an artillery shell and fired from a huge gun. We now know that the G-forces on the bodies would have killed the crew the instant the gun was fired and so the story is more than a little dated.
Wells' Martians also look exceedingly unlikely and the canals of Mars have been proven to be an optical illusion.
Orwells' Animal Farm was a thinly veiled critique of the Soviet Union, written at a time during the second world war when they were allies of the UK...yet it still got published.
Everytime an author sends out a piece of work to an agent, magazine or publisher they take a risk. So why not write something daring. If nothing else the story will stand out from the crowd.