There is a well known machlokes between the Terumas HaDeshen and Magen Avrohom (314:1) regarding a peski reisha d'lo nicha lei, on an issur d'rabonon. Although the Aruch cited in Tosafos Shabbos 103a and Kesubos 6a holds that a פסיק רישא דלא ניחא ליה is permitted even on a d'oraysa, Tosafos elaborates to prove that it is an issur d'rabonon, as does the Ran at the end of perek shemoneh sheratzim. However, when the entire melacha is only an issur d'rabonon, perhaps even Tosafos would agree that a פסיק רישא דלא ניחא ליה on an issur d'rabonon is completely permitted. The source of this discussion is when there is a knife stuck into a barrel from before shabbos and the removal of it would expand the hole and be a Rabbinic violation of making an opening, is it mutar to pull it out? It is essentially a פסיק רישא דלא ניחא ליה because he is not interested in making a pe'sach, on something which is only an issur d'rabonon. The Shulchan Aruch holds that it is permitted, and the Terumas HaDeshen explains that it is because when one does an action that as a pesik reisha results in an issur d'rabonon, but they are not at all intending for that (לא איכפת ליה), it is permitted. The Rama says that it is only permitted if it were removed before shabbos so that now it is not a pesik reisha that it will expand the hole, implying that had it been a pesik reisha, even though it is only a פסיק רישא דלא ניחא ליה on an issur d'rabonon, it is prohibited. The M.B. (11) explains that there are other factors in the case of the knife in the barrel that could affect whether it is mutar or assur, but regarding the primary question as to whether a פסיק רישא דלא ניחא ליה on an issur d'rabonon is permitted, the Magen Avrohom, Eliyahu Rabba, Gr"a and R. Akiva Eiger all hold that it is assur.
The source of this issur in the gemara is the case where one opens a door in front of a candle that causes the candle to extinguish (Rashi explains that the case is where the wind will blow it out, and Tosafos explains that the moving of the oil closer or further is a violation of burning or extinguishing). The gemara explains that even according to R. Shimon who holds that a דבר שאינו מתכוין is permitted, it would be forbidden to open the door since it is a פסיק רישא that the candle will be extinguished. The extinguishing of the candle in this situation is a מלאכה שא"צ לגופה which according to R. Shimon is only assur m'drabonon, yet the gemara says that a פסיק רישא דלא ניחא ליה would be assur. The Gr"a cites this proof that a פסיק רישא דלא ניחא ליה on an issur d'rabonon is assur, but suggests a distinction between a melacha that is inherently d'oraysa and only reduced to a d'rabonon due to מלאכה שא"צ לגופה (there is already a precedent to equate a melacha d'oraysa that is a מלאכה שא"צ לגופה with an actual d'oraysa - see Ran 94b), and a melacha which is inherently only d'rabonon. Perhaps when the melacha is inherently only d'rabonon, we would permit a פסיק רישא דלא ניחא ליה. Nevertheless, the Gr"a rejects this distinction and agrees with the Magen Avrohom that a פסיק רישא דלא ניחא ליה is assur even on an issur d'rabonon.
On the other hand, Tosafos 103a asks how the gemara in Succah can permit the removing of the berries on a hadas since it is "fixing" the hadas to be kasher and therefore should be assur as a pesik reisha. Although the gemara says that we are speaking where he has another hadas, that works well for the Aruch who permits a פסיק רישא דלא ניחא ליה, but for those who reject the Aruch, how will that gemara be explained? Tosafos answers that the fixing the hadas is only a minor tikun and therefore only a Rabbinic violation, therefore it is permitted. Tosafos implies that on an issur d'rabonon we accept the position of the Aruch that a פסיק רישא דלא ניחא ליה is permitted. This Tosafos is a strong support for the Terumas HaDeshen, however, Tosafos in other places (Kesubos, Succha) as well as other Rishonim answer the question of Tosafos differently. They say that for the sake of a mitzvah we can rely on the Aruch. The machlokes between the Terumas HaDeshen and Magen Avrohom may be a machlokes between two answers of Tosafos.
The Shulchan Aruch (336:8) writes that one shouldn't pick up a flower pot from the ground and put it on a peg, or put it from a peg back on the ground. Since the flower pot doesn't have a hole on the bottom, it is only a d'rabonon violation of planting or uprooting. The Sha'ar Hatziyun 39 says that this supports the opinion of the Magen Avrohom that a פסיק רישא דלא ניחא ליה on an issur d'rabonon is still assur.
The M.B. 321:57 cites the Magen Avrohom that one is not allowed to urinate onto dirt because of the issur gibul. Even though it is only an issur d'rabonon of gibul, it would still be forbidden. He then cites the Beis Meir who in a situation of need permits urinating directly on mud (when it is not your property so there is no interest in the gibul). The Sha'ar Hatziyun 68 explains that the heter is based on פסיק רישא דלא ניחא ליה on an issur d'rabonon. Here we see that the poskim are willing to rely on the Magen Avrohom in a makom tzorech. The Chazon Ish (58:8) writes that the heter is based on kavod habriyos and cannot be applied elsewhere.
Even according to those who are machmir like the Magen Avrohom not to permit a פסיק רישא דלא ניחא ליה even when the issur is only d'rabonon, the Sha'ar Hatziyun (316:21) cites the pri megadim that when it is a double d'rabonon, meaning two reasons why it is not d'oraysa, we can permit a פסיק רישא דלא ניחא ליה.