It would be easier to answer your question if you gave as much detail as possible about your tooth.
I am assuming the nerve isn't exposed as you would be in agony and already did whatever the dentist told you to.
I do not think protocol 1000 can be effective in halting or reversing a decaying tooth from the inside. 1000 is good at killing bacteria in the bloodstream, but the tooth is poorly supplied by the bloodstream so the MMS wouldn't get there. This is also why antibiotics cannot be used to stop bacterial tooth decay.
MMS mouthwash would kill any bacteria exposed to it directly, but it will not get through tooth enamel. Since MMS tastes so bad, you would be better off mouth washing with a mixture of some type of antiseptic essential oil (eg. clove) and perhaps black walnut tincture which is reported to strengthen tooth enamel.
If you are reluctant to do the root canal because you have heard that it can create dangers in the long term, then doing a periodic protocol 1000 after the root canal would be very effective at killing any bacteria that did seep into your bloodstream from the tooth.
Otherwise you could do the root canal procedure as usual, but instead of filling the canal with gutta percha, you could opt for some type of a highly alkaline paste before capping it. This has the advantage of continuing to kill bacteria and keep the canals clean for longer. There are several options, one of which is calcium hydroxide paste, but i'm sure there are newer ones that last longer. The key is to find one that remains alkaline for as long as possible so bacteria can't grow in the canal.
Then you could just redo the procedure every few years to ensure the canal is bacteria free if you really think this is necessary. This depends alot on where you live. If you are in Asia you could get this done cheaply, but in the states you can probably forget about that.
Your biggest challenge is finding a dentist willing to concede that there is anything dangerous about a root canal, and who will be willing to do what you ask, as opposed to the standard sodium hypochlorite for 5 mins, gutta percha and cap they learned at university.