Is there a way for Paragon Shep to keep their scars in Mass Effect 2?

No it is not possible to keep your scars the legitimate way. There is a way to remove them with the medibay upgrade but this sadly doesn't have the option to prevent them from going away.

However you could edit your savegame and increase your renegade score and I believe you will keep your scars or make them worse depending on how much renegade you add, but that wouldn't be a solution for you, based on what you've said.

It is supposedly possible to mod the coalesced.ini file to have the scars stay visible even as a paragon player. More info on that halfway down the forums here: http://social.bioware.com/forum/topic/105/index/1593065

It is possible to mod the coalesced.ini file to have the scars stay visible even as a paragon player. You'll need the Editor by Iron Spine: http://social.bioware.com/project/1854/#details
- download, extract, open it and point it to the Mass Effect 2 root folder.
- in the left panel go to BIOGame > [SFXGame.SFXPawn_Player] > Scars or just search for 'scars'
- there are 5 scar 'stages'

Scars=(Threshold=(X=-10,Y=-2),Emissive="BIOG_HMM_HED_Alignment.Emissive.Face_EmisScars_05",
Normal="BIOG_HMM_HED_Alignment.Scar.Face_NormScars_05",
EyeEmissive="BIOG_HMM_HED_Alignment.Eye.Eye_EmisScars_05",
FemaleEmissive="BIOG_HMF_HED_Alignment.Emissive.HMF_Face_EmisScars_05",
FemaleNormal="BIOG_HMF_HED_Alignment.Scar.HMF_Face_NormScars_05",
FemaleEyeEmissive="BIOG_HMF_HED_Alignment.Eye.HMF_Eye_EmisScars_05",
Color=(R=0,G=0,B=0,A=0))

Scars=(Threshold=(X=-1,Y=-1),Emissive="BIOG_HMM_HED_Alignment.Emissive.Face_EmisScars_04",
Normal="BIOG_HMM_HED_Alignment.Scar.Face_NormScars_04",
EyeEmissive="BIOG_HMM_HED_Alignment.Eye.Eye_EmisScars_04",
FemaleEmissive="BIOG_HMF_HED_Alignment.Emissive.HMF_Face_EmisScars_04"
,FemaleNormal="BIOG_HMF_HED_Alignment.Scar.HMF_Face_NormScars_04",
FemaleEyeEmissive="BIOG_HMF_HED_Alignment.Eye.HMF_Eye_EmisScars_04",
Color=(R=0,G=0,B=0,A=0))

Scars=(Threshold=(X=0,Y=0),Emissive="BIOG_HMM_HED_Alignment.Emissive.Face_EmisScars_03",
Normal="BIOG_HMM_HED_Alignment.Scar.Face_NormScars_03",
EyeEmissive="BIOG_HMM_HED_Alignment.Eye.Eye_EmisScars_03",
FemaleEmissive="BIOG_HMF_HED_Alignment.Emissive.HMF_Face_EmisScars_03",
FemaleNormal="BIOG_HMF_HED_Alignment.Scar.HMF_Face_NormScars_03",
FemaleEyeEmissive="BIOG_HMF_HED_Alignment.Eye.HMF_Eye_EmisScars_03",
Color=(R=0,G=0,B=0,A=0))

Scars=(Threshold=(X=1,Y=1),Emissive="BIOG_HMM_HED_Alignment.Emissive.Face_EmisScars_02",
Normal="BIOG_HMM_HED_Alignment.Scar.Face_NormScars_02",
EyeEmissive="BIOG_HMM_HED_Alignment.Eye.Eye_EmisScars_02",
FemaleEmissive="BIOG_HMF_HED_Alignment.Emissive.HMF_Face_EmisScars_02",
FemaleNormal="BIOG_HMF_HED_Alignment.Scar.HMF_Face_NormScars_02",
FemaleEyeEmissive="BIOG_HMF_HED_Alignment.Eye.HMF_Eye_EmisScars_02",
Color=(R=0,G=0,B=0,A=0))

Scars=(Threshold=(X=2,Y=10),Emissive="BIOG_HMM_HED_Alignment.Emissive.Face_EmisScars_01",
Normal="BIOG_HMM_HED_Alignment.Scar.Face_NormScars_01",
EyeEmissive="BIOG_HMM_HED_Alignment.Eye.Eye_EmisScars_01",
FemaleEmissive="BIOG_HMF_HED_Alignment.Emissive.HMF_Face_EmisScars_01",
FemaleNormal="BIOG_HMF_HED_Alignment.Scar.HMF_Face_NormScars_01",
FemaleEyeEmissive="BIOG_HMF_HED_Alignment.Eye.HMF_Eye_EmisScars_01",
Color=(R=0,G=0,B=0,A=0))

• the interesting part are Threshold=(X=,Y=) which means the alignement (X=-10 Y=-2 max renage; X=2,Y=10 max paragon)

EmisScars_ and NormScars_ which mean the severity of the scar graphics (05 worst, 01 healed)

• just replace the EmisScars_ and NormScars_ numbers of the alignement you want to change with the numbers of the severity you want to have.

I for example replaced 01 with 02, so even as a full paragon the scars are a little visible (tested this myself and it worked). If you replace 05 with 01 the scars should be gone even as full renegade.