The Laws have not been broken here.
The player who made the challenge has committed no offence.
The player without footwear has committed no offence as he had immediately tried to play the ball after losing his footwear.
p. 69 of the 2015/16 FIFA Laws of the Game:
If a player loses his footwear accidentally and immediately plays the ball and/or scores a goal, there is no infringement and the goal is awarded because he lost his footwear by accident.
If the referee decided that your player had committed an offence by continuing to play with the incorrect equipment for an extended period of time, they would follow this procedure on p. 23 of the 2015/16 FIFA Laws of the Game:
In the event of any infringement of this Law:
- play need not be stopped
- the player at fault is instructed by the referee to leave the field of play to correct his equipment
- the player leaves the field of play when the ball next ceases to be in play, unless he has already corrected his equipment
- any player required to leave the field of play to correct his equipment
must not re-enter without the referee’s permission
- the referee checks that the player’s equipment is correct before allowing
him to re-enter the field of play
- the player is only allowed to re-enter the field of play when the ball is out of play
If your player put himself in danger by continuing to play without footwear, he would be committing offence, and an indirect free kick would be awarded to the opponents.
p. 38 of the 2015/16 FIFA Laws of the Game:
An indirect free kick is also awarded to the opposing team if, in the opinion of the referee, a player:
- plays in a dangerous manner
However, given that the opponent was through on goal, the referee would most certainly play advantage here, otherwise he would have to send off your player for:
(p. 40, 2015/16 FIFA Laws of the Game: )
- denying an obvious goalscoring opportunity to an opponent moving towards the player’s goal by an offence punishable by a free kick or a penalty kick
On p. 35 of the 2015/16 FIFA Laws of the Game, we find the preconditions for a goal (emphasis mine):
A goal is scored when the whole of the ball passes over the goal line, between the goalposts and under the crossbar, provided that no infringement of the Laws of the Game has been committed previously by the team scoring the goal.
There was no offence by the team scoring, so the goal stands.
To address your point
This does not seem fair.
It's completely fair. The opponent did not break the Laws in challenging your player, so why should they be punished for it? It's certainly unfortunate - just like it would have been if your teammate had rolled an ankle or slipped over while chasing the defender.
If your teammate's equipment doesn't fit will enough to prevent it coming off in a challenge for the ball, he's probably most at fault for choosing equipment that is unsuitable.