rynoattack,
I understand what you're saying. Couple things when someone is a very slow runner it can sometimes appear that they are not running very hard. Your example of McGwire giving up running to 1B for injury prevention reasons might be because his power swing was not conducive to getting out of the box quickly and he was a slow runner. Only he would know for sure how many he just hit on the ground and gave up on. He did hit over 250 doubles, I'm sure he had o hustle on most of those.
Barry Bonds actually hit close to 700 doubles and triples. He also stole over 500 bases. That is a lot of chances to be injured by running. I'm sure he didn't bust it when hitting a one hopper to the second baseman, but he was only three strides out of the box when the 1Baseman caught the ball. Anyway, sometimes loafing isn't really loafing.
I know you are right about Major Leaguers taking it easy at times. Though I wouldn't call it common. At least on ground balls that are not sure outs. I just disagree with the injury reasoning for giving up. Many have played an entire career without suffering an injury running to first base. Some run fast, others run slow.