We use the imperative tense of the verb "to rest," and it sounds like a spell one of our shamanistic ancestors came up with to keep ghosts from bothering the living.

Not so. Neither the expression "rest in peace" nor the longer version "may s/he rest in peace" contains any imperative verbs. (Also, the imperative is a mood, not a tense.)

1. In the full expression, the mood is optative, not imperative. That should be clear from the examples at this link. It does not express a command; it expresses a wish.

2. English doesn't actually inflect for the optative mood; instead, optative meaning is expressed by verbs that are morphologically indistinguishable from the subjunctive or indicative verbs.

3. Link: grammar.about.com on "mood" actually uses "May he rest in peace" as an example of a sentence using the optative.

4. As for the shorter "rest in peace," it can be understood either as a truncated version of "may s/he rest in peace," in which case the verb is still optative; or it can be treated as a complete expression. If it's a complete expression then the mood is just subjunctive.

5. The English expression is a translation of the Latin Requiescat in pace, in which the verb is unambiguously subjunctive.

6. Link: grammaring.com uses "Rest in peace" as an example of a sentence with a present subjunctive.