Yes, it will have a negative effect in a number of ways.
First of all, the $2.7 billion federal cost for it will probably be accompanied by something like a $1.7 billion cost provincially and territorially, wherever other governments enact income splitting along with the federal government's program. So we're talking about $4.4 billion out of Canada's economy each year, as a minimum, that will be paid basically to reward women who put more of their efforts into unpaid work.
For women who need to have a minimum economic capacity of their own, that is, the ability to go into the labour market and earn money in some way, should life make it necessary for them to support themselves—and I think that's probably 100% of all women at some point in their lives—this means that women are essentially being bribed in a way to participate in a program that is not in their best interests.
In addition to that, people might say, “Well, women will get the benefits of income splitting too”, but there are two reasons that is not the case.
First of all, even the highest income women in this country will receive only a small proportion of those benefits compared to the men. I've done some simulation analysis using SPSD/M software produced by Statistics Canada to get these figures. Although 25% of all women in couples will get some benefit from income splitting into their own hands, they will only get 16% of the dollars. So 84% of the total $4.4 billion is going to go directly into men's hands.
The second effect that is negative for women is that there's a great deal of social research demonstrating that if a government has a choice between putting social benefits into the hands of the male in a couple or the female in a couple, or shared control over the fund, it will normally benefit the family as a whole more to give women at least half of the control over the money, if not all of it, because they tend to spend the money on things like the needs of children, the needs of the family, and so on. But if you put these tax benefits, such a huge amount of money, into the hands of men, because they will be the ones receiving sole control over the tax refunds from income splitting, then it creates a situation in which men will feel a sense of greater entitlement to decide how that money will be used, and it won't necessarily be used to meet the needs of all of the members of the household equally.