It is an established principle that when in doubt regarding a Torah law we rule stringently, whereas when in doubt regarding a Rabbinic law we rule leniently. Why is this the case? Why aren't we always stringent? Why aren't we always lenient?
First of all, there is a machlokes if Safek D'Oraisa lechumra is in fact D'Oraisa or itself a D'Rabbanan.
If its D'Oraisa, then the Torah is itself strict on such a doubt, so we may not be lenient; whereas a D'Rabbanan is subject to human rules of leeway.
If its D'rabbanan too, then we see Chazal were scared about accidentally breaking a Torah Law, but not so worried if we accidentally break a Rabbinical Law.
This seems to be because a shogeg (accidental sinner) in Torah Law, has still tainted himself with encountering the sin. So a doubt should be avoided too. But, someone who accidentally violates a Rabbinical fence or enactment, has in essence violated nothing. Alternatively, the sages were lenient about their own enactments so as not to overburden the people.
The sources are in Gemara and Poskim, but I do not have them near me now erev Pesach. I will try to edit later. But, I do remember this to be the answer talked about.
The Zohar Rakiah in Sefer HaMitzvos Shoresh Alef writes that chazal when they created their takanos, intentionally built into it the idea of suffik derabannan lekulah, in order to distinguish a derabannan from a doraisa.
This explanation makes sense if suffik doraisa lechumra is a doraisa (like the Rashba), because there is the intended distinction. However, the Zohar Rakiah is explaining the Rambam (although in a different context), who holds suffik doraisa lechumra is miderabannan. I think you'd have to say then that this was also part of the motivation to make suffik doraisa lechumra, because otherwise they'd both be lekulah, and there's be no distinction. Or at least, if something else motivated chazal to make suffik doraisa lechumra, this is why they didn't do the same for suffik derabannan.