I'm assuming both verbs are from pe'al. If so, the first sentence is better.
'to go out of' is ܢܦܩ ܡܢ, not ܣܠܩ ܡܢ.
ܣܠܩ usually means 'to go up'.
ܣܠܩ ܓܒܪܐ ܡܢ ܡܕܝܢܬܐ ܠܛܘܪܐ would mean 'The man went up from the city to the mountain.'
Similarly, ܣܠܩ ܡܢ ܬܡܢ would mean 'He went up from there.'