You really should grind out from the hole a circular area at least a couple of inches in diameter. The ground out area would resemble a shallow bowl. This bowl shape should be filled in with "discs" of light weight fiberglass cloth, the first disc would be slightly larger in diameter than the hole, each subsequent disc would be slightly larger than the previous, the last one would be the diameter of the ground out "bowl". Basically you will be filling the bowl with discs of fiberglass cloth each saturated with resin. Once the resin has hardened you can sand the surface until it's smooth, any minor recesses can be filled with a fairing compound, then finish sanded. This really isn't a big job, you can do all the fiberglassing in one go, just be sure to pre-cut your discs so you won't have to try cutting them out when your gloves are covered in resin. This job will require very small quantities of resin and glass, but it will result in a patch that is stronger than the original deck, and will last the life on the boat. Bondo might work, and would be a quick fix, but this is an automotive product and really not the best solution for a long term fix.
Zeppo is right on the money with the prep work and small circular glass pieces, however I would argue that the first disk should be the largest and smaller disks should be added from there. Adhering the largest disk will provide a better initial bond covering the entire area with one piece of continuous glass, whereas starting with the smallest one, you are only bonding the very edges of the circular pieces of fiberglass with original fiberglass material. Also, epoxy is BY FAR the best material to use for these types of repairs as the bonding strength exceeds that of standard fiberglass resin. I have done this repair many times filling in thru-hull holes on larger boats as well as much larger damaged areas like the one in the pictures below. That particular project required a different initial step as the hole was about nine inches in diameter unlike what you are describing. Click the link to see more details of this repair on my previous boat. Also, I just completed filling three holes in my "new" sunfish this way over the past week.