Elizabeth was conflicted when it came to the matter of her cousin. She knew that Mary represented danger, but she was highly aware of Mary's being a sovereign queen who was unlawfully deposed by her subjects. She could not malign her cousin at the risk of damaging the model of royal prerogative.
My dear Brother,
I would you knew (though not felt) the extreme dolor that overwhelms my mind, for that miserable accident which (far contrary to my meaning) hath befallen. I have now sent this kinsman of mine, whom ere now it hath pleased you to favour, to instruct you truly of that which is too irksome for my pen to tell you. I beseech you that as God and many more know, how innocent I am in this case : so you will believe me, that if I had bid aught I would have bid by it. I am not so base minded that fear of any living creature or Prince should make me so afraid to do that were just; or done, to deny the same. I am not of so base a lineage, nor carry so vile a mind. But, as not to disguise, fits not a King, so will I never dissemble my actions, but cause them show even as I meant them. Thus assuring yourself of me, that as I know this was deserved, yet if I had meant it I would never lay it on others' shoulders; no more will I not damnify myself that thought it not.
The circumstance it may please you to have of this bearer. And for your part, think you have not in the world a more loving kinswoman, nor a more dear friend than myself; nor any that will watch more carefully to preserve you and your estate. And who shall otherwise persuade you, judge them more partial to others than you. And thus in haste I leave to trouble you: beseeching God to send you a long reign.
Your most assured loving sister and cousin,
Clearly, Elizabeth felt that her actions were justified, but she felt somewhat wrong about it because Mary was her cousin and also a queen. I also think that Elizabeth remembered a time when she was in a similarly precarious position with her sister, Mary Tudor. Recalling that must have given her pause, if only for a moment.
I can't imagine ordering the death of a cousin, but Elizabeth was a queen. Her main priority was keeping her safety intact so as to preserve the safety of the realm. Someone once said, "It's good to be the