@Schrodinger
Rovibrational spectra are more commonly measured for simple molecules to accomplish this (because you get more pieces of information for a single experiment) and it is very easy to measure all the rotational transitions, and even discriminate isotopomers, with basic instrumentation. HCl/DCl is a common undergraduate laboratory experiment. Pure rotational spectra are not much different, though.
Note that discriminating isotopomers depends not only on spectral resolution but also the relative natural abundances of the isotopes involved.
Modern instruments have a spectral resolution on the order of ~0.001 cm-1. The spectral bandwidth of a rotational transition is on the order of ~0.01 wavenumber. No problem there - you are more likely to be limited by spectral bandwidth overlapping than instrumental shortcomings.
Turning to CO:
Based on natural abundances (NA) of the various nuclei, only three permutations of CO really need be considered. 12C-16O (NA ~ 98.65%), 12C-18O (NA ~ 0.2%), and 13C-16O (NA ~ 1.1%). All remaining combinations have NA values below 0.05%.
The rotational constant B of 12C-16O can be easily estimated by calculating the moment of inertia from molecular weights and bond lengths to be ~ 8.7247 amu Å2. The analogous values for 12C-18O and 13C-17O are 9.1612 and 9.1260. From these values, the respective rotational constants are ~1.932 cm-1, ~ 1.8404 cm-1 and ~1.847 cm-1, respectively. Take as an example the E(J=7) to E(J=8) rotational transition, which occurs at a value of 14B. For 12C-16O, 12C-18O, and 13C-16O the transition energies are therefore predicted to be ~27.050 cm-1, ~25.762 cm-1, ~25.858 cm-1, respectively. Given the bandwidths of these transitions and even allowing for a much poorer instrument resolution, there should be no trouble distinguishing the intense transitions of 12C-16O from the other to isotopomers. However, 25.762 and 25.858 cm-1 are <0.01 cm-1 separated, on the order of the peak widths. Coupled with the fact that they are expected to be weak, owing to low abundance, it is predictable that it will be hard to resolve these peaks.
This is exactly what you see in the pure rotational spectrum of CO, shown below from Spectra of Atoms and Molecules by Bernath (Figure 6.15, p 172). Note the little peaks in between the big peaks that correspond to the overlapped transitions from low NA isotopomers. You might be able to convince yourself by their symmetry that they are the overlap of two peaks. But they are so weak that spectral deconvolution would be difficult. Resolving these peaks may be possible by making other adjustments to the experiment.
So, yes you can resolve isotopomers using even basic pure rotational spectroscopy (and rovibrational spectroscopy) provided their reduced masses are sufficiently different from each other.