plan to send his subconscious back to know not to do it.
nah, he actually pulled his subconsciousness FORWARD by embedding the program into the machine itself. There was no going backwards.. they just pulled the present Peter forward so he would see how awful his actions would make things.. and since Walter is the one that builds the machine, he was the one that built it into the machine for when Peter got into it in the present.
He has a conversation with Walter about him just not sending the machine of the first men back in the first place. Its interesting that he claims he can't do that because he has already done it or some shite.
Step on a cockroach and kill a boy in china 15 years later.. for all Walter knew, it was the very event of him sending the machine back in time that caused the universes to split, he couldn't justify NOT sending it back once he realized it was him who had done it.. I would actually gander to say that at the end of season 3, we see the full force of multiple timelines finally coming together.. every timeline had another walter more intelligent, and more able to create a more sophisticated machine.. after going through this cycle: 3,4,15 times? He finally perfected being able to pull Peter's conscience to the future.
FWIW: I really think the reason they didn't just "not send the machine back" was because they knew if nothing else, by pulling Peter to the future, it would fix things.