Yes, there will be products to make this simpler, but the point is, unless you are willing to grant LetsEncrypt a DV cert monopoly, to the exclusion of all others (or at least those not compatible with their API), then, in general, it can never be as easy as just turning it on.
DNSSEC puts the CA monopoly in the DNS. There is no API for a hypothetical web server using DANE, because there's no need for periodic domain validation. Of course, DNSSEC is a disaster, so it's a non-starter... but I'm still going to lament the fact that everything is terrible.
Since LetsEncrypt's API protocol is being standardized through the IETF (https://tools.ietf.org/html/draft-ietf-acme-acme), there's no reason any new competing free certificate providers can't be compatible with it. In the long term, if more show up (and I wouldn't be surprised if some existing CAs refocus their business on EV and start offering free DV certs through ACME), I see no problem with software giving the protocol a "monopoly", in the sense of building in auto-configuration support for it.
DNSSEC puts the CA monopoly in the DNS. There is no API for a hypothetical web server using DANE, because there's no need for periodic domain validation. Of course, DNSSEC is a disaster, so it's a non-starter... but I'm still going to lament the fact that everything is terrible.