stm32L0 - can I use LSE clock for 1ms tick and use HSI for systick?
Of course, you able to use two clock sources.
Read Reference manual (RM0377, http://www.st.com/web/en/resource/technical/document/reference_manual/DM00108282.pdf), section Reset and clock controls.

Core and peripherals will work with HSI, multiplied by PLL (if you want work on frequency, not equal to 16MHz), and RTC will be clocked by low-speed crystal.

Also, if you don't needed power saving features, you may use only one high-speed crystal (8 MHz, for example), and feed clock via PLL to core  and via prescaler - to RTC. You may find details in ref.manual, figure 'Clock tree (STM32F03x and STM32F05x devices)'.

PS you may use RTC wakeup interrupt instead of systick timer. This will provide more accurate period measurements.