Do these two sentences mean the same?
Knowing that I hurt you is breaking my heart.
If I know I hurt you, it is breaking my heart.
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The second sentence is not grammatically correct, and thus doesn't really mean anything.
It could be made grammatically correct by changing to
I know I hurt you, and it is breaking my heart.
which would mean the same thing as the first, as dropping the if makes it a declarative statement, not a conditional.
If you changed it to
If I knew I hurt you, it would break my heart
now it is a conditional (you don't know you hurt them, but if you did, it would break your heart) and it doesn't mean the same as the original.