1. Second base is the farthest from the catcher, which makes it the easiest base to steal.
2. Reaching 2B puts a runner in scoring position, so it's important to the offense to get him there and important to the defense to keep him on 1B.
3. That's why 1B is (almost always) the only base where the runner is held on.
4. More runners reach 1B than any other base.

All of these points apply only to 1B, which explains why it's treated differently. The intent of the rules is to balance offense and defense with respect to advancing a runner to 2B.

If the rules don't allow for a warning, then you don't get one. While I can't say whether the rule was properly applied by the umpires going off your description of the event, I do know that this is a case where coaches and players don't get a warning.

I hope you have statistics to prove that bold statement :D

Evans has explained that his research indicates that even the early rules makers understood that scoring was more exciting than not scoring. The rules regarding first actually lean heavily towards the offense to protect the runner and provide a greater chance of scoring.