Your post contained two slightly different rules issues -- malicious contact and Force Play Slide Rule.
The rule you quoted seems to be the same as teh NCAA malicious contact rule -- it applies only when there is malicious contact / a blocked base, etc. It *usually* does not apply on a double-play ball / slide at second (that is, it could apply, but instances of "crashing maliciously" into F4 / F6 are rare).
The rule you paraphrased (slide directly into the bag) seems to be the same as the FED and NCAA FPSR. Failing to slide in this manner does result in two outs.
Since you didn't describe the actions of R1 during the play, I can't comment on what I think the appropriate ruling would be.
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