NOTE: The following calculations are a Fermi Approximation only. They contain some small but inconsequential errors. The orders of magnitude stated are accurate.
In order for a planet to survive, the incoming energy from the supernova must be significantly less than the binding energy of the planet. If the energy delivered to a planet is higher than the binding energy then the planet blows up, à la Alderaan. A blown up planet has zero value as a shield for a piddly little $3 \, \text{km}$ spaceship.
Supernova energy output: $10^{44} \,\text{to}\, 2 \cdot 10^{44} \,\text{J}$.
Binding Energy of Earth: $2.41 \cdot 10^{32} \,\text{J}$
Binding Energy of Jupiter: $2.086 \cdot 10^{35} \,\text{J}$
Surface area of Jupiter exposed to blast: $\frac{61.42 \,\text{billion km}^2}{2} = 30.71 \,\text{billion km}^2$
Distance from Sun to Jupiter: $778.5 \,\text{million km}$
From the Inverse Square law, we lose 9 orders of magnitude in intensity between $0.05 \,\text{million km}$ from the supernova point source and $778.5 \,\text{million km}$ leaving us with
Intensity = $\frac{1}{(7.785 \cdot 10^{8} \, \text{km})^2}$
So, at Jupiter's distance from the Sun, we should expect an energy delivery of $10^{44} \,\text{J} \cdot \frac{1}{(7.785 \cdot 10^{8} \, \text{km})^2} = 1.6499955 \cdot 10^{26} \, \frac{\text{J}}{\text{km}^{2}}$
Jupiter, with an area of $1.61 \cdot 10^{10} \, \text{km}^{2}$ will receive $\frac{1.61 \cdot 10^{10} \, \text{km}^2}{7.62 \cdot 10^{18} \, \text{km}^2} = 2.11286089 \cdot 10^{-9}$
(where $7.62 \cdot 10^{18} \, \text{km}^{2}$ is the surface area of the spherical blast front with a radius of Jupiter's distance to the Sun)
for a total of $1.6499955 \cdot 10^{26} \, \frac{\text{J}}{\text{km}^{2}} \cdot 2.11286089 \cdot 10^{-9} = 3.4845888 \cdot 10^{17} \, \frac{\text{J}}{\text{km}^{2}}$
Back to the Orders of Magnitude table, energies in the $10^{17}$ range are equivalent to the Tsar Bomba rated at 50 megatons.
Roughly every square kilometer of Jupiter is getting hit with the largest nuclear weapon that man has ever made. (There we go, those are the mind blowing numbers I was expecting.)
While $3.4845888 \cdot 10^{17} \, \text{J}$ is significantly below the binding energy of Jupiter and Earth, getting hit with that much energy will do extremely unpredictable things to Jupiter's atmosphere and orbit. I don't have the math to figure out those kind of calculations but anywhere near a supernova is going to be a really uncomfortable place to live.
Possibly, if the ship bedded down deeply in Jupiter's atmosphere on the far side of star, it might survive. Maybe. If Jupiter's core gets a huge shove outward (which it very well may) then the ship may get pushed too far into Jupiter's gravity well and experience a hull failure because of the insane pressures. Or (I'm speculating and definitely don't have the math to prove it) that much energy will kick off a chain of thermonuclear reactions in Jupiter's core that will incinerate the ship.
And the procrastinators don't get on. Anyone who caused this kind of procrastination deserves a Darwin fate as they are too stupid to live.