Yes it's an MPR violation.  The sub cannot be removed prior to completing MPR.

Starter cannot re-enter until his sub has completed (essentially) MPR.

Sub cannot re-enter.

Therefore because the sub was removed he cannot re-enter and because the sub did not complete MPR the starter cannot re-enter.

The "next pitch or play" doesn't apply to improper subs - see 4.19(d)

Yes - the call was correct.

Shouldn't we be going to the LL tournament rules to resolve the OP's situation??

The clue:  Given, the OP is talking MPR three(3) defensive outs, it appears it was a Williamsport T-game.

Regular season Rule  4.19(d)  giving way to #10(c)--page T-19.---and T-Rules re "PROTESTS"---[where its noted the T-Rule replaces regular season Rule 4.19]---top of page T-11.

Frank!

Where's the "delete" key?

Under T-protest rules--page T-11......the DA's ruling is  not necessarily the "FINAL" decision....unless BOTH managers accept his/her ruling.

If not, the protest moves up the Chain of Command to the TC in  Williamsport at the request of the protesting manager.

In the case presented by the OP.... ONLY the visiting--[offending]- team manager--[-as reported in the OP]-- agreed to accept the DA'a ruling.

If the home team (protesting) manager was of the "mind' in seeking a more stringent penalty---For Ex: a foreit ruling---he/she could reject the DA's ruling.

[not saying the TC would rule a forfeit----but, the possibility exists]

Indeed, per the OP, within the rules, the protesting manager DID NOT accept the TD's decision, moving the protest on to the next person in the Chain of Command----the DA.

As far as the protest having to be made "before the next pitch or play"-----in the case of a manager's failure to meet the MPR requirements, an MPR violation supported by Rule 10(c)--page T-19------[which appears to be the case presented by the OP]----the home team  manager's  protest can be made before the umpires leave the field. Note 3, page T-11.  Flying in the face of Note 1. same page.

Frank!

PB: Agreed----there does exist two issues in the OP's scenario..... cited #1 & #2 below, this post.  Re an illegal sub requiring a protest before the next pitch or play.

The OP wrote the starter re-entered illegally on defense at the bottom of the 3rd, and completed the inning.

The opportunity for a protest before "the next pitch or play"----WAS  apparently  correctly ruled on.

The 2011 rule change you cited, allowing Williamsport to take action  involving an MPR violation is in bold type on page T-18.

Now, IMO--- hypothetically, absent 10(f) being a factor in the OP's scenario, the protesting manager would have had the luxury of choosing one of two(2) rule "weapons" options as support for filing a protest.

Viz:

1)---Illegal substitution----before the next pitch or play.

OR---

2)---MPR violation before the umpires leave the field.

     And if the potential protesting manager, because he won the game, chooses not to file an MPR protest; then the TC, if the MPR violation is brought to THEIR attention..... say, for example, by a delegated game TD.   By the wording in the new rule.... the TC can levy sanctions/penalties against the offending manager absent any input from an offended manager.

Back to reality, IMO--: In the OP's scenario, #2 (above) would better serve the protesting manager.

Frank!

LL has been very clear that a starter can leave before he meets MPR, a sub can not. A sub has to meet all parts of the MPR before being removed.