I am on prescription progesterone suppositories. It is the only reason I have dd today - I spotted to 15 weeks with her, bright red, every day. The suspected problem, based on bloodwork and prior miscarriages, is that (for me) the corpus luteum simply doesn't produce sufficient progesterone to keep a pregnancy. So the only way to keep it is to supplement with more progesterone. Having a short LP was another indicator of this insufficiency.
The progesterone in the cream is probably the same as the prescription progesterone I'm taking - I just get more with the prescription. I took it from 6 wks to 15 wks with my last pregnancy.
There really isn't anything unnatural about progesterone - it is the same chemical that your body naturaly produces. And there is a pretty wide range of normal, so if supplementing actually brings you above "average" it's still likely you're in the normal range. And if you actually do need it, then it's probably bringing you up into the normal range.
There is some evidence that progesterone may be associated with a small increase in birth defects, but my hypothesis is that those pregnancies might have been terminated by the body because there was something minor already wrong with them, and the progesterone made them stick - not that the progesterone caused the birth defects. That is just my theory, but there is honestly not a whole lot of information about the effect of supplemental progesterone in early pregnancy. I personally, based on research and experience, believe it is harmless and probably the only way I can carry a baby past the first trimester (when the placenta takes over production of progesterone from the corpus luteum). To be safe, I take the progesterone until 15-16 wks.
I would not worry about continuing the progesterone cream. My super-natural family practitioner was very happy to write a prescription for me as soon as I found out I was pregnant.