Combine pomegranate juice, ginger, thyme, orange zest and juice, honey, and cloves in a medium saucepan over medium heat. Bring to a simmer and cook until the mixture has reduced by half, about 10 minutes.
Add blueberries and continue cooking, stirring occasionally, until sauce is concentrated and slightly thickened, about 8 to 10 minutes. Remove from heat and season with salt and lemon juice. Cool and serve lukewarm or chilled, garnished with pomegranate seeds.