Interesting theory.
A disadvantage would be Venus's circular orbit. You'd expect something coming in like that to be more elliptical, taking a lot longer than the time suggested to settle into its current orbit, which is the most circular of any planet in our system - less that 1% elliptic.
It is arguable that Uranus is also retrograde, depending which way up you define it.
Also, Venus has a well-formed high-pressure atmosphere; again, I'd expect that to take longer to form.
I'm no expert, but the sudden intrusion of something that large into the Solar System would probably have slightly more effect on us than a couple of frogs and a completely localized and very temporary parting of a specific part of the sea. I would expect significantly more than even the Biblical flood. I'd also suggest that if you are going to believe the Bible stories as written but look for "natural" causes, that'll take more faith than believing in God in the first place. I mean, how lucky would that have made Moses and the Israelites?!
Moses: "Well, it looks as though God doesn't exist, but a huge new planet ripped through the sky just as those pesky Egyptians were closing in on us, parted the sea allowing is to run through unharmed but then collapsed on the Egyptian army. Obviously, no-one will believe that, so we're sticking with the God story."
Sigh - I'd better respond to pjd, although this is off-topic here. Firstly, if Yam Suf were just a reedy marsh, why did the entire Egyptian army perish chasing a ragged bunch of ex-slaves? Secondly, the chariot and horses of fire separated aging Elijah from replacement Elisha, then Elijah was taken up to heaven in a whirlwind (2 Kings 2:11). Seems hard to believe that a meteor strike could take one man away but leave his companion unhurt and suitable for many years more work... As for the non-frog plagues, explaining away the whole lot as a package gets difficult. Agree with disruption point; not sure about a major meteor strike changing spin direction without smashing up the planet.