Personally, I cannot see how the principle of double effect would justify continued sexual practice while on the Pill for noncontraceptive reasons. From Wikipedia, the criteria for judging whether or not the principle of double effect can legitimize an action:
the nature of the act is itself good, or at least morally neutral;
the agent intends the good effect and not the bad either as a means to the good or as an end itself;
the good effect outweighs the bad effect in circumstances sufficiently grave to justify causing the bad effect and the agent exercises due diligence to minimize the harm. (Double-Effect Reasoning: Doing Good and Avoiding Evil, p.36, Oxford: Clarendon Press, T. A. Cavanaugh)
The good effect, in this case, is the mitigation of troublesome symptoms and the ability to continue practicing marital sex; the bad effect is, potentially, the destruction of one’s unborn child.
The good effect clearly does not outweight the bad there. And the agent can exercise due diligence to minimize harm by remaining abstinent and thus avoiding the potentially abortifacient effect of the Pill entirely.
Thus it seems to me that to continue sexual practice while on the Pill is not in fact justifiable even by good intentions.