Once the torso of the suit is assembled, drill a hole in the ball which the foot connects to. If you're careful you should be able to drill a hole about 5mm deep without much trouble. I use a 0.8mm or 1mm drill bit.
Next, push the feet onto the legs so the two parts snap together. At this point, do not use any glue on the joint between the legs and the feet. Only use glue on the bottom of the feet, and put the model on the base, leaving it to dry for a good while so there is nice strong joint.
Once the glue is totally dry, carefully unclip the rest of the model from the feet. Now you have the feet glued to the base in the perfect position for the pose of your suit (hopefully your pose is more interesting than mine!) and you can see exactly where you need to drill the holes for your pins.
Get your hobby drill and extend the bit out so that it is long enough to drill down into the hole in the top of the foot and out through the bottom of the base.
Now it's time to glue the pin onto the base. I use dressmaking pins just because I had a box in the house the first time I ever decided to pin something and I found that they did the job fine. Straightened out paperclips or brass wire would work fine too.
Feed to the two pins up through the bottom of the base and superglue them in place. Dressmaking pins work very well here because the flat part at the top of the pushes against the underside of the base and helps to make a nice solid glue joint. The pins can then be trimmed to the correct length.
Now all that's left is to put some superglue on the other end of the pins, some plastic cement on the ankle joints and carefully push the model onto its feet and the base, making sure that the pins go nicely into the holes that you drilled in the legs.
Once this is dry the model should be nicely reinforced and a lot less likely to break off the ankles if it falls off the table.
The pin is visible from the back of the model, though it could easily be hidden with some creative basing. Personally I don't bother because I don't find it too offensive.