Plenty of discussion has gone into whether intentionally conceded safeties should be part of the game.
As the rules stand, it is the smart thing to do on a 3rd down deep in your own end. Many have suggested rule changes that would promote punting and making a defensive stand as opposed to deliberately conceding points to mitigate the likelihood of a field goal. These have included moving the goal posts back or forcing the conceding team to give a free punt or kickoff from deep in their own end regardless.
In the late 19th century and early 20th century, football adopted major rule changes almost every year as the game quickly evolved from rugby to the gridiron. This included the scoring system. Field goals were once more valuable than a try (touchdown).
Has anyone suggested making the safety 3 points?
This would make it pointless to intentionally give up points as you would already be giving up 3 points and giving up the chance of a missed FG, block or turnover. You also would eliminate intentionally conceded points without changing any significant aspect of the game. You would also add value to a rare defensive feat should a defense be successful in bringing the ball carrier down in the end zone.