"To handle certificates is..." vs. "handling certificates is..."

Solution 1:

The sentence that starts with the gerund handling is far preferable in my opinion.

In general, starting English sentences off with infinitives leads to awkward-sounding sentences, though it certainly does happen. ("Being or not being, that is the question" somehow has less force to it...)

Solution 2:

I would say that "Handling certificates manually is time consuming and expensive" reads better.

If you wish to use the infinitive, I'd suggest "It is time consuming and expensive to handle certificates manually" - but, in my opinion, this is still less elegant than the first example.