If I was actually capable of self-modification like that, and the only other part of me trying to control what I did was my consequentialist module, I would do it, But really, that would increase the willpower costs of taking/not taking actions my consequentialist module wants to take/not take anyway, and make me less moral overall as a greater fraction of my motivations became selfish ones.
If I was actually capable of self-modification like that
On our current hardware, you're not: removing the "deontology module" isn't really an option. However, you probably are capable of removing or changing the rules that your "deontology module" (probably not an actual module) is following. In order to feel guilty about things, you have to have experiences of guilt that have been associated to patterns of behavior, and such experiential memories are pretty open to being manipulated after the fact.
That aside, though, the reasoning...
I notice that a large fraction of Effective Altruism people are vegetarian. This makes sense: in general Effective Altruists take moral issues seriously, even when that means changing your lifestyle. I'm not sure it's a good balance, though.
One way to think about this is to convert it into money. How much would I need to be paid to give up eating meat? All animal products? How much money would I need to spend on myself to be about as happy as I would be with less money but continuing to eat animals? I'd probably be willing to go vegetarian for about $500/year, vegan for maybe $2000/year.
It turns out you can probably pay to convince other people to be vegetarian much more cheaply than that. I estimate the cost of a vegetarian-year at $4.29 to $536 while Brian Tomasik estimates $11 with better methodology (which I looked at). This is by placing ads on facebook for a site where people can watch an animial cruelty video and ideally become vegetarian or vegan.
If you would get more than $11/year worth of enjoyment out of continuing to eat meat, why not give $11/year to convince someone else to not eat meat for you? Or give $50/year and be on the safe side?
(While you're giving money, you should probably give it to the organization that you think will do the most good with it, which I think is probably one of GiveWell's top charities. The nice thing about money as opposed to actions is that it's easy to redirect.)
I also posted this on my blog.