On one of my computer, there is hyper-threading enabled. Is there a way to make Boinc run only one process per actual core?

By default BOINC will use all cores that you allow through preferences and run one task per core, if the application is single threaded and not multi threaded.

If you only want to use the physical cores only you'll have to disable hyperthreading through the BIOS/UEFI. BOINC has no way of knowing which core is physical or virtual.

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In Windows this is fairly easy to do without disabling HT for the CPU by using the start /AFFINITY command line.

For example if you has an i3 that was 2c/4t You could use this command line to have only the CPU cores used:
start /affinity 5 notepad.exe

For BOINC you would also need to modify the number of CPUs it uses.
By either setting your BOINC Computing Prefs to "Use at most X% of the CPUs " to 50% or by using <ncpus>x</ncpus> in your cc_config.xml.

When I was testing this with my i7-860 my preference was to set <ncpus> to 4 and then start BOINC with an affinity mask of 55.