Ion beam therapy offers the possibility of a highly conformal tumor-dose distribution; however, this technique is extremely sensitive to inaccuracies in the treatment procedures. Ambiguities in the conversion of Hounsfield units of the treatment planning x-ray CT to relative stopping power (RSP) can cause uncertainties in the estimated ion range of up to several millimeters. Ion CT (iCT) represents a favorable solution allowing to directly assess the RSP. In this simulation study we investigate the performance of the integration-mode configuration for carbon iCT, in comparison with a single-particle approach under the same set-up. The experimental detector consists of a stack of 61 air-filled parallel-plate ionization chambers, interleaved with 3 mm thick PMMA absorbers. By means of Monte Carlo simulations, this design was applied to acquire iCTs of phantoms of tissue-equivalent materials. An optimization of the acquisition parameters was performed to reduce the dose exposure, and the implications of a reduced absorber thickness were assessed. In order to overcome limitations of integration-mode detection in the presence of lateral tissue heterogeneities a dedicated post-processing method using a linear decomposition of the detector signal was developed and its performance was compared to the list-mode acquisition. For the current set-up, the phantom dose could be reduced to below 30 mGy with only minor image quality degradation. By using the decomposition method a correct identification of the components and a RSP accuracy improvement of around 2.0% was obtained. The comparison of integration- and list-mode indicated a slightly better image quality of the latter, with an average median RSP error below 1.8% and 1.0%, respectively. With a decreased absorber thickness a reduced RSP error was observed. Overall, these findings support the potential of iCT for low dose RSP estimation, showing that integration-mode detectors with dedicated post-processing strategies can provide a RSP accuracy comparable to list-mode configurations.